6SHR | pdb_00006shr

X-RAY CRYSTAL STRUCTURE OF CELL-FREE PROTEIN SYNTHESIS (CFPS) PRODUCED SDF1-A

PDB DOI: https://doi.org/10.2210/pdb6SHR/pdb

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

Deposited: 2019-08-08 Released: 2020-08-26
Deposition Author(s): Jugnarain, V.M., Mitchell, E., Forsyth, T., Michael, H., Cortes, S., Tillier, B.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.239 (Depositor), 0.250 (DCC)
R-Value Work:
0.191 (Depositor), 0.196 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

X-RAY CRYSTAL STRUCTURE OF CELL-FREE PROTEIN SYNTHESIS (CFPS) PRODUCED SDF1-A

Jugnarain, V.M., Mitchell, E.

To be published.

Macromolecule Content

Total Structure Weight: 7.57 kDa
Atom Count: 591
Modeled Residue Count: 64
Deposited Residue Count: 64
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromal cell-derived factor 1	A	64	Homo sapiens	Mutation(s): 0 Gene Names: CXCL12, SDF1, SDF1A, SDF1B
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens) Explore P48061 Go to UniProtKB: P48061
PHAROS: P48061 GTEx: ENSG00000107562
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48061
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.239 (Depositor), 0.250 (DCC)
R-Value Work: 0.191 (Depositor), 0.196 (DCC)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.989	α = 90
b = 55.989	β = 90
c = 45.487	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Jugnarain, V.M.

Funding Organization	Location	Grant Number
French National Research Agency	France	2014/1049

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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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.