1WVP | pdb_00001wvp

Structure of chemically modified myoglobin with distal N-tetrazolyl-histidine E7(64)

• PDB DOI: https://doi.org/10.2210/pdb1WVP/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Physeter macrocephalus
• Mutation(s): Yes 


• Deposited: 2004-12-23 Released: 2005-01-18 
• Deposition Author(s): Makino, M., Sugimoto, H., Kamiya, N., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Heme environmental structure of a novel artificial myoglobin with a closed heme pocket: site-specific chemical modification producing distal N-tetrazolylhistidine E7 by cyanogen bromide and azide ion

Kamiya, N., Shiro, Y., Iwata, T., Iizuka, T., Iwasaki, H.

(1991) J Am Chem Soc 113: 1826-1829

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.09 kDa 
• Atom Count: 1,461 
• Modeled Residue Count: 151 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Physeter macrocephalus	Mutation(s): 1  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NZH	A	L-PEPTIDE LINKING	C7 H9 N7 O		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.982	α = 90
b = 60.982	β = 90
c = 84.808	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Makino, M., Sugimoto, H., Kamiya, N., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description