3LTL | pdb_00003ltl

Crystal structure of human BIG1 Sec7 domain

PDB DOI: https://doi.org/10.2210/pdb3LTL/pdb

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

Deposited: 2010-02-16 Released: 2011-04-13
Deposition Author(s): Simister, P.C., Joubert, A., Cherfils, J., Biou, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.236 (Depositor), 0.233 (DCC)
R-Value Work:
0.175 (Depositor), 0.169 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3LTL

This is version 1.2 of the entry. See complete history.

Literature

The Sec7 domain structures of human BIG1 and Cytohesin1 Arf nucleotide exchange factors

Zeeh, J.C., Simister, P.C., Rousseau, V., Joubert, A., Cherfils, J., Biou, V.

To be published.

Macromolecule Content

Total Structure Weight: 48.92 kDa
Atom Count: 3,142
Modeled Residue Count: 377
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Brefeldin A-inhibited guanine nucleotide-exchange protein 1	A, B	211	Homo sapiens	Mutation(s): 0 Gene Names: ARFGEF1, ARFGEP1, BIG1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6D6 (Homo sapiens) Explore Q9Y6D6 Go to UniProtKB: Q9Y6D6
PHAROS: Q9Y6D6 GTEx: ENSG00000066777
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y6D6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236 (Depositor), 0.233 (DCC)
R-Value Work: 0.175 (Depositor), 0.169 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.451	α = 90
b = 36.867	β = 90.06
c = 85.848	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.