4OLE | pdb_00004ole

Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution

PDB DOI: https://doi.org/10.2210/pdb4OLE/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-01-23 Released: 2014-02-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 56.32 kDa
Atom Count: 4,587
Modeled Residue Count: 480
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Next to BRCA1 gene 1 protein	A, B, C, D	122	Homo sapiens	Mutation(s): 0 Gene Names: 1A13B, BC009808, KIAA0049, M17S2, MIG19, NBR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14596 (Homo sapiens) Explore Q14596 Go to UniProtKB: Q14596
PHAROS: Q14596 GTEx: ENSG00000188554
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	E [auth A] F [auth A] G [auth A] K [auth B] L [auth B] E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth D] Focus chain R [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain P [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C]	H [auth A] I [auth A] J [auth A] M [auth B] N [auth C] H [auth A], I [auth A], J [auth A], M [auth B], N [auth C], O [auth C], P [auth C], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.173 (Depositor), 0.180 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34OLE

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.457	α = 90
b = 111.457	β = 90
c = 230.607	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
BUSTER	refinement