6GY4 | pdb_00006gy4

Crystal structure of the N-terminal KH domain of human BICC1

PDB DOI: https://doi.org/10.2210/pdb6GY4/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-06-28 Released: 2018-07-18
Deposition Author(s): Newman, J.A., Katis, V.L., Shrestha, L., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.303 (Depositor), 0.295 (DCC)
R-Value Work:
0.256 (Depositor), 0.256 (DCC)
R-Value Observed:
0.258 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6GY4

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

Literature

Crystal structure of the N-terminal KH domain of human BICC1

Newman, J.A., Katis, V.L., Shrestha, L., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 39.84 kDa
Atom Count: 2,310
Modeled Residue Count: 293
Deposited Residue Count: 344
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein bicaudal C homolog 1	A, B, C, D	86	Homo sapiens	Mutation(s): 0 Gene Names: BICC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H694 (Homo sapiens) Explore Q9H694 Go to UniProtKB: Q9H694
PHAROS: Q9H694 GTEx: ENSG00000122870
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H694
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XPE Query on XPE Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C₂₀ H₄₂ O₁₁ DTPCFIHYWYONMD-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth C] SDF format, chain G [auth C] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C]	E [auth B], F [auth C], G [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.303 (Depositor), 0.295 (DCC)
R-Value Work: 0.256 (Depositor), 0.256 (DCC)
R-Value Observed: 0.258 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.406	α = 90
b = 153.164	β = 90
c = 86.235	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Burgess-Brown, N.

Arrowsmith, C.H.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2018-07-18
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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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.