BMRBj - BMREntryMaster

Found 1 Document (0.723 seconds)

BMRB: 36001

5B7J

Structure model of a protein-DNA complex

Authors

Jin, C., Hu, Y., Ding, J., Zhang, Y.

Assembly

Switch-activating protein 1/DNA Complex

Entity

1. Switch-activating protein 1/DNA Complex, entity 1 (polymer), 111 monomers, 13223.02 Da Detail

AKAQRTHLSL EEKIKLMRLV VRHKHELVDR KTSEFYAKIA RIGYEDEGLA IHTESACRNQ IISIMRVYEQ RLAHRQPGMK TTPEEDELDQ LCDEWKARLS ELQQYREKFL V

2. Switch-activating protein 1/DNA Complex, entity 2 (polymer, Thiol state: not present), 12 monomers, 3701.404 Da Detail

CAAAACAATA TT

3. Switch-activating protein 1/DNA Complex, entity 3 (polymer, Thiol state: not present), 12 monomers, 3745.396 Da Detail

AATATTGTTT TG

Total weight

20669.82 Da

Max. entity weight

13223.02 Da

Source organism

Schizosaccharomyces pombe 972h- , Schizosaccharomyces pombe

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 82.2 %, Completeness: 66.2 %, Completeness (bb): 72.2 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	66.2 % (1053 of 1590)	53.4 % (507 of 949)	84.7 % (443 of 523)	87.3 % (103 of 118)
Backbone	72.2 % (599 of 830)	49.1 % (192 of 391)	93.6 % (309 of 330)	89.9 % (98 of 109)
Sidechain	63.9 % (555 of 868)	56.5 % (315 of 558)	78.1 % (235 of 301)	55.6 % (5 of 9)
Aromatic	28.8 % (38 of 132)	22.2 % (20 of 90)	41.5 % (17 of 41)	100.0 % (1 of 1)
Methyl	71.2 % (94 of 132)	66.2 % (47 of 71)	77.0 % (47 of 61)

1. entity 1

AKAQRTHLSL EEKIKLMRLV VRHKHELVDR KTSEFYAKIA RIGYEDEGLA IHTESACRNQ IISIMRVYEQ RLAHRQPGMK TTPEEDELDQ LCDEWKARLS ELQQYREKFL V

2. entity 2

CAAAACAATA TT

3. entity 3

AATATTGTTT TG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM [U-99% 15N][U-99% 13C; U-99% 15N] Sap1, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Sap1	[U-99% 15N][U-99% 13C; U-99% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	DNA (5'-CAAAACAATATT-3')	natural abundance	0.5 mM
8	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
9	sodium phosphate	natural abundance	20 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5B7J, Strand ID: A Detail

Release date

2016-07-04

Citation

Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe
Guan, L., He, P., Yang, F., Zhang, Y., Hu, Y., Ding, J., Hua, Y., Zhang, Y., Ye, Q., Hu, J., Wang, T., Jin, C., Kong, D.
J. Biol. Chem. (2017), 292, 6056-6075, PubMed 28223353 , DOI 10.1074/jbc.M116.767806 , Abstract

Related entities 1. Switch-activating protein 1/DNA Complex, entity 1, : 2 : 1 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM [U-99% 15N][U-99% 13C; U-99% 15N] Sap1, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Sap1	[U-99% 15N][U-99% 13C; U-99% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM

2 3D 1H-15N NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

3 3D 1H-13C NOESY

Instrument

Bruker Avance - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	DNA (5'-CAAAACAATATT-3')	natural abundance	0.5 mM
8	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
9	sodium phosphate	natural abundance	20 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

6 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sap1	[U-99% 15N][U-99% 13C; U-99% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM

8 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sap1	[U-99% 15N][U-99% 13C; U-99% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM

9 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

10 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

11 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

12 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sap1	[U-99% 15N][U-99% 13C; U-99% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM

13 3D filtered NOESY

Instrument

Bruker Avance - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
3	DNA (5'-CAAAACAATATT-3')	natural abundance	0.7 mM
4	DNA (5'-GTTTTGTTATAA-3')	natural abundance	0.0 ~ 0.0 mM
5	Sap1	[U-99% 13C; U-99% 15N]	0.5 mM
6	sodium phosphate	natural abundance	20 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_36001_5b7j.nef
Input source #2: Coordindates	5b7j.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

----30--------40--------50--------60--------70--------80--------90-------100-------110-------120----
AKAQRTHLSLEEKIKLMRLVVRHKHELVDRKTSEFYAKIARIGYEDEGLAIHTESACRNQIISIMRVYEQRLAHRQPGMKTTPEEDELDQLCDEWKARLS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AKAQRTHLSLEEKIKLMRLVVRHKHELVDRKTSEFYAKIARIGYEDEGLAIHTESACRNQIISIMRVYEQRLAHRQPGMKTTPEEDELDQLCDEWKARLS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---130-----
ELQQYREKFLV
|||||||||||
ELQQYREKFLV
-------110-

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

-------210--
CAAAACAATATT
||||||||||||
CAAAACAATATT
--------10--

Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C

-----220----
AATATTGTTTTG
||||||||||||
AATATTGTTTTG
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	111	100.0
B	B	12	100.0
C	C	12	100.0

Content subtype: combined_36001_5b7j.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1050		99.1 (chain: A, length: 111)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	231 (1)	undefined	91.7 (chain: B, length: 12), 91.7 (chain: C, length: 12)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	8 (1)	noe	25.0 (chain: B, length: 12)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	73 (1)	noe	9.0 (chain: A, length: 111), 33.3 (chain: B, length: 12), 58.3 (chain: C, length: 12)
4	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	38 (1)	hbond	100.0 (chain: B, length: 12), 100.0 (chain: C, length: 12)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	157 (157)	.	100.0 (chain: B, length: 12), 100.0 (chain: C, length: 12)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 514
  - ¹³C chemical shifts: 438
  - ¹⁵N chemical shifts: 98
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	719	514	71.5
¹³C chemical shifts	523	438	83.7
¹⁵N chemical shifts	129	98	76.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	223	193	86.5
¹³C chemical shifts	222	204	91.9
¹⁵N chemical shifts	109	93	85.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	496	321	64.7
¹³C chemical shifts	301	234	77.7
¹⁵N chemical shifts	20	5	25.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	49	76.6
¹³C chemical shifts	64	48	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	22	52.4
¹³C chemical shifts	41	17	41.5
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 91.7%
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 91.7%
- Total number of restraints: 231
- Weight of restraints: 1.0 (231)
- Potential type of restraints: square-well-parabolic (231)
- Range of distance target values: 7.0, 38.7 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
  - Chain_ID: C
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 25.0%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: square-well-parabolic (8)
  - Range of distance target values: 3.65, 4.15 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 9.0%
      - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 33.3%
      - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 58.3%
    - Total number of restraints: 71
    - Weight of restraints: 1.0 (71)
    - Potential type of restraints: square-well-parabolic (71)
    - Range of distance target values: 3.15, 4.4 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
      - Chain_ID: C
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_2
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
        -------210-- CAAAACAATATT |||||||||||| CAAAACAATATT
        Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 100.0%
        -----220---- AATATTGTTTTG |||||||||||| AATATTGTTTTG
      - Total number of restraints: 38
        Total hydrogen bond restraints: 38
      - Weight of restraints: 1.0 (38)
        Total hydrogen bond restraints: 1.0 (38)
      - Potential type of restraints: square-well-parabolic (38)
        Total hydrogen bond restraints: square-well-parabolic (38)
      - Range of distance target values: 1.82, 2.95 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        None
        Chain_ID: B
        Chain_ID: C
      - Distance restraints on contact map
        Chain_ID_1: B - Chain_ID_2: B
        None
        Chain_ID_1: C - Chain_ID_2: C
        None
        Chain_ID_1: B - Chain_ID_2: C

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 157
- Total number of restraints per polymer type: 157
- Weight of restraints: 1.0 (157)
- Potential type of restraints: square-well-parabolic (157)
- Dihedral angle restraints per residue
  - Chain_ID: B
  - Chain_ID: C

Keywords DNA, DNA BINDING PROTEIN-DNA complex, complex, interaction, protein

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.723 seconds)

BMRB: 36001

Sample #1

Sample #2

Sample #3

Related entities 1. Switch-activating protein 1/DNA Complex, entity 1, : 2 : 1 entities Detail

Experiments performed 13 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail