4JON | pdb_00004jon

Crystal structure of a centrosomal protein 170kDa, transcript variant beta (CEP170) from Homo sapiens at 2.15 A resolution (PSI Community Target, Sundstrom)

PDB DOI: https://doi.org/10.2210/pdb4JON/pdb

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

Deposited: 2013-03-18 Released: 2013-04-17
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.203 (Depositor), 0.200 (DCC)
R-Value Work:
0.183 (Depositor), 0.180 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a centrosomal protein 170kDa, transcript variant beta (CEP170) from Homo sapiens at 2.15 A resolution (PSI Community Target, Sundstrom)

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 73.01 kDa
Atom Count: 5,185
Modeled Residue Count: 605
Deposited Residue Count: 635
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centrosomal protein of 170 kDa	A, B, C, D, E	127	Homo sapiens	Mutation(s): 0 Gene Names: CEP170, FAM68A, KAB, KIAA0470, NM_001042404
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SW79 (Homo sapiens) Explore Q5SW79 Go to UniProtKB: Q5SW79
PHAROS: Q5SW79 GTEx: ENSG00000143702
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SW79
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.203 (Depositor), 0.200 (DCC)
R-Value Work: 0.183 (Depositor), 0.180 (DCC)
R-Value Observed: 0.184 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34JON

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.04	α = 90
b = 183.332	β = 90
c = 97.268	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-04-17
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-05-22
Changes: Data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.