1H7K

Formation of a tyrosyl radical intermediate in Proteus mirabilis catalase by directed mutagenesis and consequences for nucleotide reactivity

Structural Biology Knowledgebase: 1H7K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.237

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1H7K

Classification: OXIDOREDUCTASE

Total Structure Weight: 56383.40

Macromolecule Entities
Molecule Chains Length Organism Details
CATALASE A 483 Proteus mirabilis EC#: 1.11.1.6 IUBMB
Mutation: F215Y, M53X
Details: METHIONINE SULFONE IN POSITION 53, TYROSINE 337 LACK THE HYDROXYL HYDROGEN
Gene Name(s): katA

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
OMT
Query on OMT
A L-PEPTIDE LINKING C5 H11 N O4 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.237
  • Space Group: P 62 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.00 α = 90.00
b = 110.00 β = 90.00
c = 251.20 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-07-08
  • Released Date: 2004-02-25
  • Deposition author(s): Andreoletti, P., Gambarelli, S., Gaillard, J., Sainz, G., Stojanoff, V., Jouve, H.M.

Revision History

  • 2015-09-16
    Type: Version format compliance | Details: REMARK 4
  • 2015-09-16
    Type: Polymer description | Details: COMPND
  • 2015-09-16
    Type: Entry authorship | Details: AUTHOR
  • 2015-09-16
    Type: Refinement description | Details: REMARK 3
  • 2015-09-16
    Type: Source and taxonomy | Details: SOURCE
  • 2015-09-16
    Type: Non-polymer description | Details: HETSYN,FORMUL
  • 2015-09-16
    Type: Geometry validation | Details: REMARK 500
  • 2015-09-16
    Type: Function and keywords | Details: KEYWDS
  • 2015-09-16
    Type: Secondary structure | Details: HELIX,SHEET
  • 2015-09-16
    Type: Citation | Details: REMARK 1,JRNL
  • 2015-09-16
    Type: Other | Details: REMARK 375,REMARK 900,REMARK 100,REMARK 525,MASTER
  • 2015-09-16
    Type: Biological assembly | Details: REMARK 300,REMARK 350