4XDX | pdb_00004xdx

The crystal structure of soluble human interleukin 8 expressed in Pichia pastoris

• PDB DOI: https://doi.org/10.2210/pdb4XDX/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2014-12-20 Released: 2015-12-23 
• Deposition Author(s): Ostrov, D.A., Pompeu, Y.A., Jakoncic, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.136 (Depositor), 0.138 (DCC) 
• R-Value Work: 
  0.121 (Depositor) 
• R-Value Observed: 
  0.122 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of soluble human interleukin 8 expressed in Pichia pastoris

Ostrov, D.A., Pompeu, Y.A., Jakoncic, J.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.24 kDa 
• Atom Count: 818 
• Modeled Residue Count: 70 
• Deposited Residue Count: 70 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-8	A	70	Homo sapiens	Mutation(s): 0  Gene Names: CXCL8, IL8
UniProt & NIH Common Fund Data Resources
Find proteins for P10145 (Homo sapiens) Explore P10145  Go to UniProtKB:  P10145
PHAROS:  P10145 GTEx:  ENSG00000169429

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.136 (Depositor), 0.138 (DCC) 
• R-Value Work:  0.121 (Depositor) 
• R-Value Observed: 0.122 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.093	α = 90
b = 40.093	β = 90
c = 89.269	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
Coot	model building
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Ostrov, D.A., Pompeu, Y.A., Jakoncic, J.J.

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary