7BJI | pdb_00007bji

Crystal structure of the Danio rerio centrosomal protein Cep135 coiled-coil fragment 64-190

PDB DOI: https://doi.org/10.2210/pdb7BJI/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Danio rerio
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-14 Released: 2021-01-27
Deposition Author(s): Li, Q., Hatzopoulos, G., Iller, O., Vakonakis, I.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free:
0.249 (Depositor), 0.259 (DCC)
R-Value Work:
0.233 (Depositor), 0.239 (DCC)
R-Value Observed:
0.234 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the Danio rerio centrosomal protein Cep135 coiled-coil fragment 64-190

Li, Q., Hatzopoulos, G., Iller, O., Vakonakis, I.

To be published.

Macromolecule Content

Total Structure Weight: 60.67 kDa
Atom Count: 2,968
Modeled Residue Count: 344
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centrosomal protein of 135 kDa	A, B, C, D	129	Danio rerio	Mutation(s): 0 Gene Names: cep135, si:dkeyp-117h8.1
UniProt
Find proteins for Q5RG45 (Danio rerio) Explore Q5RG45 Go to UniProtKB: Q5RG45
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5RG45
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	G [auth A] H [auth A] J [auth A] K [auth B] L [auth B] G [auth A], H [auth A], J [auth A], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain N [auth C]	E [auth A], N [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.249 (Depositor), 0.259 (DCC)
R-Value Work: 0.233 (Depositor), 0.239 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.29	α = 90
b = 188.22	β = 90
c = 89.97	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
pointless	data scaling
SHELXDE	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Hatzopoulos, G.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N009274/1

Revision History (Full details and data files)

Version 1.0: 2021-01-27
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.