BMRBj - BMREntryMaster

Found 1 Document (0.71 seconds)

BMRB: 16024

2KAJ

NMR structrure of gallium subsituted ferredoxin

Authors

Xu, X., Ubbink, M., Knaff, D.B.

Assembly

Ga-substituted Ferredoxin

Entity

1. Ferredoxin (polymer, Thiol state: free and other bound), 96 monomers, 10231.99 Da Detail

ASYTVKLITP DGESSIECSD DTYILDAAEE AGLDLPYSCR AGACSTCAGK ITAGSVDQSD QSFLDDDQIE AGYVLTCVAY PTSDCTIETH KEEDLY

2. GA (non-polymer), 69.723 Da

Total weight

10301.713 Da

Max. entity weight

10231.99 Da

Source organism

Synechocystis sp. PCC 6803

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.7 %, Completeness (bb): 99.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	98.7 % (590 of 598)	98.6 % (495 of 502)	99.0 % (95 of 96)
Backbone	99.0 % (285 of 288)	99.0 % (193 of 195)	98.9 % (92 of 93)
Sidechain	98.4 % (305 of 310)	98.4 % (302 of 307)	100.0 % (3 of 3)
Aromatic	90.3 % (28 of 31)	90.3 % (28 of 31)
Methyl	98.1 % (52 of 53)	98.1 % (52 of 53)

1. Ferredoxin

ASYTVKLITP DGESSIECSD DTYILDAAEE AGLDLPYSCR AGACSTCAGK ITAGSVDQSD QSFLDDDQIE AGYVLTCVAY PTSDCTIETH KEEDLY

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GaFd	[U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM

Sample #2

Solvent system 99%D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
3	GaFd	natural abundance		2 mM
4	sodium phosphate	natural abundance		50 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2KAJ, Strand ID: A Detail

Release date

2010-07-26

Citation

Structural and functional characterization of the ga-substituted ferredoxin from Synechocystis sp. PCC6803, a mimic of the native protein
Xu, X., Scanu, S., Chung, J., Hirasawa, M., Knaff, D.B., Ubbink, M.
Biochemistry (2010), 49, 7790-7797, PubMed 20690702 , DOI 10.1021/bi100712g , Abstract

Related entities 1. Ferredoxin, : 1 : 5 : 3 : 210 entities Detail

Interaction partners 1. Ferredoxin, : 4 interactors Detail

More details for 4 interactors identified by 4 citations

Experiments performed 5 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16024_2kaj.nef
Input source #2: Coordindates	2kaj.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:44:CYS:SG	2:1:GA:GA	unknown	unknown	n/a
1:47:CYS:SG	2:1:GA:GA	unknown	unknown	n/a
1:77:CYS:SG	2:1:GA:GA	unknown	unknown	n/a
1:39:CYS:SG	2:1:GA:GA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	GA	GALLIUM (III) ION	Distance restraints

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90------
ASYTVKLITPDGESSIECSDDTYILDAAEEAGLDLPYSCRAGACSTCAGKITAGSVDQSDQSFLDDDQIEAGYVLTCVAYPTSDCTIETHKEEDLY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ASYTVKLITPDGESSIECSDDTYILDAAEEAGLDLPYSCRAGACSTCAGKITAGSVDQSDQSFLDDDQIEAGYVLTCVAYPTSDCTIETHKEEDLY

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0

Content subtype: combined_16024_2kaj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	590		100.0 (chain: A, length: 96)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	4 (1)	undefined	4.2 (chain: A, length: 96), 100.0 (chain: B, length: 1)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2763 (1)	noe	100.0 (chain: A, length: 96)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	17 (1)	noe	22.9 (chain: A, length: 96)
4	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	4 (1)	undefined	4.2 (chain: A, length: 96), 100.0 (chain: B, length: 1)
5	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	36 (1)	hbond	26.0 (chain: A, length: 96)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 494
  - ¹⁵N chemical shifts: 96
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
90	HIS	HD1	7.058

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	502	493	98.2
¹⁵N chemical shifts	97	96	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	195	193	99.0
¹⁵N chemical shifts	93	92	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	307	300	97.7
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	52	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	28	90.3

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 4.2%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 4
- Weight of restraints: 1.0 (4)
- Potential type of restraints: upper-bound-parabolic (4)
- Range of distance target values: 2.2, 2.2 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 100.0%
  - Total number of restraints: 2763
  - Weight of restraints: 1.0 (2763)
  - Potential type of restraints: upper-bound-parabolic (2763)
  - Range of distance target values: 2.52, 6.72 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 22.9%
    - Total number of restraints: 17
    - Weight of restraints: 1.0 (17)
    - Potential type of restraints: upper-bound-parabolic (17)
    - Range of distance target values: 4.5, 5.5 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_5
      - Status: Warning
      - Experiment type: undefined
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 4.2%
        Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
        - X | X
      - Total number of restraints: 4
        Total other bond restraints: 4
      - Weight of restraints: 1.0 (4)
        Total other bond restraints: 1.0 (4)
      - Potential type of restraints: upper-bound-parabolic (4)
        Total other bond restraints: upper-bound-parabolic (4)
      - Range of distance target values: 2.4, 2.4 (Å)
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
      - Distance restraints on contact map
        Chain_ID_1: B - Chain_ID_2: B
        None
      - Saveframe: DYANA/DIANA_distance_constraints_4
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 26.0%
        Total number of restraints: 36
        Total hydrogen bond restraints: 36
        O...H-x: 3
        O...h-N: 3
        Long range: 30
        O...H-x: 15
        O...h-N: 15
        Weight of restraints: 1.0 (36)
        Total hydrogen bond restraints: 1.0 (36)
        O...H-x: 1.0 (3)
        O...h-N: 1.0 (3)
        Long range: 1.0 (30)
        O...H-x: 1.0 (15)
        O...h-N: 1.0 (15)
        Potential type of restraints: upper-bound-parabolic (36)
        Total hydrogen bond restraints: upper-bound-parabolic (36)
        O...H-x: upper-bound-parabolic (3)
        O...h-N: upper-bound-parabolic (3)
        Long range: upper-bound-parabolic (30)
        O...H-x: upper-bound-parabolic (15)
        O...h-N: upper-bound-parabolic (15)
        Range of distance target values: 2.4, 3.3 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Distance restraints on contact map

Keywords ferredoxin, iron-sulfur

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 (0.71 seconds)

BMRB: 16024

Sample #1

Sample #2

Related entities 1. Ferredoxin, : 1 : 5 : 3 : 210 entities Detail

Interaction partners 1. Ferredoxin, : 4 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail