6VDX

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Manganese(III)- Porphyrin and Substrate Trichlorophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme

McGuire, A.H.Petit, A.R.Kang, J.Malewschik, T.de Serrano, V.Carey, L.M.Ghiladi, R.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehaloperoxidase B
A, B
137Amphitrite ornataMutation(s): 0 
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata)
Explore Q9NAV7 
Go to UniProtKB:  Q9NAV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NAV7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MNR (Subject of Investigation/LOI)
Query on MNR

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
PROTOPORPHYRIN IX CONTAINING MN
C34 H32 Mn N4 O4
UAPHVASSHGRKEN-RGGAHWMASA-L
T6C (Subject of Investigation/LOI)
Query on T6C

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C [auth A],
J [auth B]
2,4,6-trichlorophenol
C6 H3 Cl3 O
LINPIYWFGCPVIE-UHFFFAOYSA-N
PEG
Query on PEG

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E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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H [auth A],
I [auth A],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

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D [auth A],
F [auth A],
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.365α = 90
b = 67.585β = 90
c = 67.626γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-04-03
    Changes: Refinement description