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Found 1 Document (2.335 seconds)

BMRB: 25232

2MUT

Solution structure of the F231L mutant ERCC1-XPF dimerization region

Authors

Faridounnia, M., Wienk, H., Kovacic, L., Folkers, G.E., Jaspers, N.GJ., Kaptein, R., Hoeijmakers, J.HJ., Boelens, R.

Assembly

F231L mutant ERCC1-XPF dimerization region

Entity

1. F231L mutant ERCC1-XPF dimerization region, entity 1 (polymer), 96 monomers, 10965.50 Da Detail

RIRRRYNMAD LLMEKLEQDL VSRVTECLTT VKSVNKTDSQ TLLTTFGSLE QLIAASREDL ALCPGLGPQK ARRLFDVLHE PFLKVPGGLE HHHHHH

2. F231L mutant ERCC1-XPF dimerization region, entity 2 (polymer), 84 monomers, 9217.408 Da Detail

MDSETLPESE KYNPGPQDFL LKMPGVNAKN CRSLMHHVKN IAELAALSQD ELTSILGNAA NAKQLYDFIH TSFAEVVSKG KGKK

Total weight

20182.908 Da

Max. entity weight

10965.5 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

restrained molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.7 %, Completeness: 88.2 %, Completeness (bb): 93.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.2 % (1853 of 2102)	88.5 % (971 of 1097)	86.7 % (709 of 818)	92.5 % (173 of 187)
Backbone	93.1 % (991 of 1064)	93.6 % (339 of 362)	92.5 % (490 of 530)	94.2 % (162 of 172)
Sidechain	84.9 % (1025 of 1208)	86.0 % (632 of 735)	83.4 % (382 of 458)	73.3 % (11 of 15)
Aromatic	58.1 % (72 of 124)	66.1 % (41 of 62)	50.0 % (31 of 62)
Methyl	95.6 % (197 of 206)	96.1 % (99 of 103)	95.1 % (98 of 103)

1. entity 1

RIRRRYNMAD LLMEKLEQDL VSRVTECLTT VKSVNKTDSQ TLLTTFGSLE QLIAASREDL ALCPGLGPQK ARRLFDVLHE PFLKVPGGLE HHHHHH

2. entity 2

MDSETLPESE KYNPGPQDFL LKMPGVNAKN CRSLMHHVKN IAELAALSQD ELTSILGNAA NAKQLYDFIH TSFAEVVSKG KGKK

Show sample condition

Sample

Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 290 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.4 mM
2	entity_2	[U-100% 13C; U-100% 15N]	0.4 mM
3	D2O	natural abundance	8 %
4	H2O	natural abundance	92 %
5	sodium phosphate	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.23 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MUT, Strand ID: A, B Detail

Release date

2015-06-21

Citation

The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex
Faridounnia, M., Wienk, H., Kovacic, L., Folkers, G.E., Jaspers, N.GJ., Boelens, R.
J. Biol. Chem. (2015), 290, 20541-20555, PubMed 26085086 , DOI 10.1074/jbc.M114.635169 , Abstract

Related entities 1. F231L mutant ERCC1-XPF dimerization region, entity 1, : 2 : 12 entities Detail

Related entities 2. F231L mutant ERCC1-XPF dimerization region, entity 2, : 1 : 2 : 2 : 13 entities Detail

Interaction partners 1. F231L mutant ERCC1-XPF dimerization region, entity 1, : 21 : 1 interactors Detail

More details for 22 interactors identified by 10 citations

Interaction partners 2. F231L mutant ERCC1-XPF dimerization region, entity 2, : 24 : 1 interactors Detail

More details for 25 interactors identified by 10 citations

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25232_2mut.nef
Input source #2: Coordindates	2mut.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

------220-------230-------240-------250-------260-------270-------280-------290-------300-------
RIRRRYNMADLLMEKLEQDLVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVPGGLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RIRRRYNMADLLMEKLEQDLVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVPGGLEHHHHHH
--------10--------20--------30--------40--------50--------60--------70--------80--------90------

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

------830-------840-------850-------860-------870-------880-------890-------900-----
MDSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK
--------10--------20--------30--------40--------50--------60--------70--------80----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0
B	B	84	0	0	100.0

Content subtype: combined_25232_2mut.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1838		94.8 (chain: A, length: 96), 98.8 (chain: B, length: 84)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	5101 (1)	noe	94.8 (chain: A, length: 96), 98.8 (chain: B, length: 84)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	126 (1)	hbond	56.2 (chain: A, length: 96), 51.2 (chain: B, length: 84)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	267 (267)	.	83.3 (chain: A, length: 96), 84.5 (chain: B, length: 84)

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: 94.8%
  - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 98.8%
- Total number of assignments
  - ¹H chemical shifts: 971
  - ¹³C chemical shifts: 695
  - ¹⁵N chemical shifts: 172
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	589	501	85.1
¹³C chemical shifts	443	355	80.1
¹⁵N chemical shifts	106	87	82.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	193	180	93.3
¹³C chemical shifts	192	164	85.4
¹⁵N chemical shifts	92	84	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	396	321	81.1
¹³C chemical shifts	251	191	76.1
¹⁵N chemical shifts	14	3	21.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	56	90.3
¹³C chemical shifts	62	56	90.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	16	48.5
¹³C chemical shifts	33	9	27.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	508	470	92.5
¹³C chemical shifts	375	340	90.7
¹⁵N chemical shifts	90	85	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	169	165	97.6
¹³C chemical shifts	168	158	94.0
¹⁵N chemical shifts	80	77	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	339	305	90.0
¹³C chemical shifts	207	182	87.9
¹⁵N chemical shifts	10	8	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	45	97.8
¹³C chemical shifts	46	44	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	25	86.2
¹³C chemical shifts	29	22	75.9

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 94.8%
  - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 98.8%
- Total number of restraints: 5101
- Weight of restraints: 1.0 (5101)
- Potential type of restraints: square-well-parabolic (5101)
- Range of distance target values: 1.16, 3.02 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 56.2%
    - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 51.2%
  - Total number of restraints: 126
  - Weight of restraints: 1.0 (126)
  - Potential type of restraints: square-well-parabolic (126)
  - Range of distance target values: 2.05, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 83.3%
  - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 84.5%
- Total number of restraints: 267
- Total number of restraints per polymer type: 267
- Weight of restraints: 1.0 (267)
- Potential type of restraints: square-well-parabolic (267)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords ERCC1-XPF, F231L, Nucleotide Excision Repair

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Found 1 Document (2.335 seconds)

BMRB: 25232

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. F231L mutant ERCC1-XPF dimerization region, entity 1, : 2 : 12 entities Detail

Related entities 2. F231L mutant ERCC1-XPF dimerization region, entity 2, : 1 : 2 : 2 : 13 entities Detail

Interaction partners 1. F231L mutant ERCC1-XPF dimerization region, entity 1, : 21 : 1 interactors Detail

Interaction partners 2. F231L mutant ERCC1-XPF dimerization region, entity 2, : 24 : 1 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

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Sample

Instrument

Sample

NMR combined restraints 5 contents Detail