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

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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), 0.200 (DCC) 

Starting Model: experimental

Literature

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

Jugnarain, V.M., Mitchell, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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

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), 0.200 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Jugnarain, V.M., Mitchell, E., Forsyth, T., Michael, H., Cortes, S., Tillier, B.

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

Revision History  

• 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