4DWU

Carbonmonoxy dehaloperoxidase-hemoglobin A structure at 1.44 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb4DWU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Amphitrite ornata
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-26 Released: 2013-02-27
Deposition Author(s): de Serrano, V.S., Zhao, J., Franzen, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free:
0.202 (Depositor), 0.200 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A unique role for the distal histidine observed in carbonmonoxy dehaloperoxidase-hemoglobin A structures

de Serrano, V.S., Zhao, J., Franzen, S.

To be published.

Macromolecule Content

Total Structure Weight: 32.87 kDa
Atom Count: 3,360
Modelled Residue Count: 274
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase A	A, B	137	Amphitrite ornata	Mutation(s): 0 Gene Names: dhpA EC: 1.11
UniProt
Find proteins for Q9NAV8 (Amphitrite ornata) Explore Q9NAV8 Go to UniProtKB: Q9NAV8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NAV8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
CMO Query on CMO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.202 (Depositor), 0.200 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.922	α = 90
b = 67.622	β = 90
c = 68.391	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-02-27

Deposition Author(s):

de Serrano, V.S.

Zhao, J.

Franzen, S.

Revision History (Full details and data files)

Version 1.0: 2013-02-27
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description