5C7Y | pdb_00005c7y

ZHD-Intermediate complex after ZHD crystal soaking in ZEN for 9min

  • Classification: HYDROLASE
  • Organism(s): Clonostachys rosea
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-06-25 Released: 2016-06-29 
  • Deposition Author(s): Hu, X.-J., Qi, Q., Yang, W.-J.
  • Funding Organization(s): Chinese High-tech Research and Development program, the 973 Program of the Ministry of Science and Technology of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.181 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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

Literature

A Case Study of Lactonase ZHD

Ming, D.-M., Qi, Q., Yang, W.-J., Sun, K.-L., Xu, T.-Y., Huang, Q., Hu, X.-J., Lv, H.

To be published.

Macromolecule Content 

  • Total Structure Weight: 63.12 kDa 
  • Atom Count: 4,859 
  • Modeled Residue Count: 533 
  • Deposited Residue Count: 568 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zearalenone hydrolase
A, B
284Clonostachys roseaMutation(s): 0 
Gene Names: zhd101
EC: 3.1.1
UniProt
Find proteins for Q8NKB0 (Bionectria ochroleuca)
Explore Q8NKB0 
Go to UniProtKB:  Q8NKB0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NKB0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZFR

Query on ZFR


Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]		(1E,10S)-1-(3,5-dihydroxyphenyl)-10-hydroxyundec-1-en-6-one
C17 H24 O4
TVXRLKRGDWQGQV-MXPWBENCSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
D [auth A],
I [auth B],
J [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT

Query on FMT


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
K [auth B]		FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
K

Query on K


Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.181 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.69α = 90
b = 89.67β = 90
c = 113.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese High-tech Research and Development programChina2013AA102803B
Chinese High-tech Research and Development programChina2014AA021301
the 973 Program of the Ministry of Science and Technology of ChinaChinaNo. 2009CB918602

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description