2V5F

Crystal structure of wild type peptide-binding domain of human type I collagen prolyl 4-hydroxylase.

• PDB DOI: https://doi.org/10.2210/pdb2V5F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-10-06 Released: 2009-11-17 
• Deposition Author(s): Pekkala, M., Hieta, R., Kivirikko, K., Myllyharju, J., Wierenga, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.265 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Crystal Structure of Wild Type Peptide-Binding Domain of Human Type I Collagen Prolyl 4- Hydroxylase.

Pekkala, M., Hieta, R., Kivirikko, K., Myllyharju, J., Wierenga, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.93 kDa 
• Atom Count: 995 
• Modelled Residue Count: 103 
• Deposited Residue Count: 110 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1	A	104	Homo sapiens	Mutation(s): 0  EC: 1.14.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for P13674 (Homo sapiens) Explore P13674  Go to UniProtKB:  P13674
PHAROS:  P13674 GTEx:  ENSG00000122884

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEXA-HISTIDINE PEPTIDE	B [auth X]	6	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.265 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.472	α = 90
b = 59.046	β = 90
c = 61.668	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Pekkala, M., Hieta, R., Kivirikko, K., Myllyharju, J., Wierenga, R.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2016-12-21
  Changes: Source and taxonomy, Structure summary
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description