2XF2 | pdb_00002xf2

PVC-AT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.173 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HDDClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 1.7 of the entry. See complete history. 


Literature

X-Ray Investigation of Penicillium Vitale Catalase Inhibited by Aminotriazole

Borovik, A., Grebenko, A.I., Melik-Adamyan, W.R.

(2011) Crystallogr Rep 56: 590


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATALASEA,
B [auth E]		688Penicillium janthinellumMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for D9N167 (Penicillium janthinellum)
Explore D9N167 
Go to UniProtKB:  D9N167
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9N167
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HDD
Query on HDD
Download Ideal Coordinates CCD File 
C [auth A],
K [auth E]		CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
C34 H32 Fe N4 O5
UMGOPAWIGKFTRK-QQDQPIDJSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
L [auth E]
M [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
3TR
Query on 3TR
Download Ideal Coordinates CCD File 
G [auth A],
O [auth E]		3-AMINO-1,2,4-TRIAZOLE
C2 H4 N4
KLSJWNVTNUYHDU-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
P [auth E]
Q [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.173 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.3α = 90
b = 144.3β = 90
c = 133.8γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HDDClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-08-24
    Changes: Non-polymer description, Other, Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Data collection, Database references
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations
  • Version 1.4: 2019-10-16
    Changes: Data collection, Experimental preparation, Other
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.7: 2024-11-06
    Changes: Structure summary