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Found 1 Document (1.592 seconds)

BMRB: 15240

2JPD

Solution structure of the ERCC1 central domain

Authors

Tripsianes, K., Folkers, G., Zheng, C., Das, D., Grinstead, J.S., Kaptein, R., Boelens, R.

Assembly

ERCC1 central

Entity

1. ERCC1 central (polymer, Thiol state: all free), 135 monomers, 15437.63 Da Detail

MAKSNSIIVS PRQRGNPVLK FVRNVPWEFG DVIPDYVLGQ STCALFLSLR YHNLHPDYIH GRLQSLGKNF ALRVLLVQVD VKDPQQALKE LAKMCILADC TLILAWSPEE AGRYLETYKA YEQKPGGLEH HHHHH

Formula weight

15437.63 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.1 %, Completeness: 84.0 %, Completeness (bb): 78.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.0 % (1362 of 1621)	90.4 % (763 of 844)	73.7 % (469 of 636)	92.2 % (130 of 141)
Backbone	78.7 % (625 of 794)	90.7 % (245 of 270)	66.2 % (263 of 397)	92.1 % (117 of 127)
Sidechain	89.7 % (856 of 954)	90.2 % (518 of 574)	88.8 % (325 of 366)	92.9 % (13 of 14)
Aromatic	76.4 % (113 of 148)	82.4 % (61 of 74)	69.4 % (50 of 72)	100.0 % (2 of 2)
Methyl	95.0 % (152 of 160)	95.0 % (76 of 80)	95.0 % (76 of 80)

1. ERCC1 central

MAKSNSIIVS PRQRGNPVLK FVRNVPWEFG DVIPDYVLGQ STCALFLSLR YHNLHPDYIH GRLQSLGKNF ALRVLLVQVD VKDPQQALKE LAKMCILADC TLILAWSPEE AGRYLETYKA YEQKPGGLEH HHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 290 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	ERCC1 central	[U-13C; U-15N]	0.8 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 290 K, pH 5.5

#	Name	Isotope labeling	Concentration
4	ERCC1 central	[U-15N]	0.8 mM
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	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.0 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2007-08-27

Citation

Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization
Tripsianes, K., Folkers, G.E., Zheng, C., Das, D., Grinstead, J.S., Kaptein, R., Boelens, R.
Nucleic Acids Res. (2007), 35, 5789-5798, PubMed 17720715 , DOI 10.1093/nar/gkm503 , Abstract

Related entities 1. ERCC1 central, : 1 : 4 : 22 entities Detail

Interaction partners 1. ERCC1 central, : 22 interactors Detail

More details for 22 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_15240_2jpd.nef
Input source #2: Coordindates	2jpd.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

---100-------110-------120-------130-------140-------150-------160-------170-------180-------190----
MAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADC
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---200-------210-------220---------
TLILAWSPEEAGRYLETYKAYEQKPGGLEHHHHHH
|||||||||||||||||||||||||||||||||||
TLILAWSPEEAGRYLETYKAYEQKPGGLEHHHHHH
-------110-------120-------130-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	135	0	0	100.0

Content subtype: combined_15240_2jpd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1324		91.9 (chain: A, length: 135)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	5044 (1)	noe	94.8 (chain: A, length: 135)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	62 (1)	hbond	34.1 (chain: A, length: 135)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	174 (174)	.	86.7 (chain: A, length: 135)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 91.9%
- Total number of assignments
  - ¹H chemical shifts: 756
  - ¹³C chemical shifts: 443
  - ¹⁵N chemical shifts: 125
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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	844	756	89.6
¹³C chemical shifts	636	443	69.7
¹⁵N chemical shifts	148	125	84.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	270	244	90.4
¹³C chemical shifts	270	122	45.2
¹⁵N chemical shifts	127	114	89.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	574	512	89.2
¹³C chemical shifts	366	321	87.7
¹⁵N chemical shifts	21	11	52.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	79	96.3
¹³C chemical shifts	82	79	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	57	77.0
¹³C chemical shifts	72	46	63.9
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 94.8%
- Total number of restraints: 4968
- Weight of restraints: 1.0 (4968)
- Potential type of restraints: square-well-parabolic (4968)
- Range of distance target values: 2.17, 3.77 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- 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: 135, Sequence coverage: 34.1%
  - Total number of restraints: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: square-well-parabolic (62)
  - Range of distance target values: 2.05, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: 135, Sequence coverage: 86.7%
- Total number of restraints: 174
- Total number of restraints per polymer type: 174
- Weight of restraints: 1.0 (174)
- Potential type of restraints: square-well-parabolic (174)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (1.592 seconds)

BMRB: 15240

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ERCC1 central, : 1 : 4 : 22 entities Detail

Interaction partners 1. ERCC1 central, : 22 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail