5VTT | pdb_00005vtt

Dehaloperoxidase B Y38F mutant

PDB DOI: https://doi.org/10.2210/pdb5VTT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Amphitrite ornata
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-05-18 Released: 2018-05-23
Deposition Author(s): Carey, L.M., Ghiladi, R.A.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.166 (Depositor), 0.168 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Probing the Structure-Function Relationship of a Multifunctional Enzyme using Crystallographic Diffraction Methods

Carey, L.M.

(2017) Thesis

Macromolecule Content

Total Structure Weight: 32.38 kDa
Atom Count: 2,493
Modeled Residue Count: 274
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase B	A, B	137	Amphitrite ornata	Mutation(s): 1
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata) Explore Q9NAV7 Go to UniProtKB: Q9NAV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NAV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.166 (Depositor), 0.168 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.663	α = 90
b = 67.689	β = 90
c = 67.862	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-23

Deposition Author(s):

Carey, L.M.

Ghiladi, R.A.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-05-23
Type: Initial release
Version 1.1: 2019-04-03
Changes: Data collection, Database references
Version 1.2: 2019-11-27
Changes: Author supporting evidence, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description