5BV2

Crystal structure of E. coli HPII catalase variant

• PDB DOI: https://doi.org/10.2210/pdb5BV2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-04 Released: 2015-06-24 
• Deposition Author(s): Wang, J., Lomkalin, I.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.132 
• R-Value Work: 0.082 
• R-Value Observed: 0.085 

Starting Model: experimental

Literature

Influence of weak-intensity data, ordered water molecules, and hydrogen atoms on the refinement of a large protein crystal structure

Wang, J., Lomkalin, I.V.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 344.49 kDa 
• Atom Count: 29,414 
• Modelled Residue Count: 2,987 
• Deposited Residue Count: 3,012 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase HPII	A [auth P], B [auth Q], C [auth R], D [auth S]	753	Escherichia coli	Mutation(s): 0  EC: 1.11.1.6
UniProt
Find proteins for P21179 (Escherichia coli (strain K12)) Explore P21179  Go to UniProtKB:  P21179

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HDD	E [auth P], HB [auth S], VA [auth R], W [auth Q]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C34 H32 Fe N4 O5 UMGOPAWIGKFTRK-QQDQPIDJSA-N
PG4	GB [auth R]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	BB [auth R], CB [auth R], P	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	R [auth P], RA [auth Q], S [auth P], SA [auth Q], T [auth P], TA [auth Q], U [auth P], UA [auth Q], WB [auth S], XB [auth S]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	UB [auth S], V [auth P]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	DB [auth R], EB [auth R], F [auth P], IB [auth S], PA [auth Q], Q [auth P], QA [auth Q], SB [auth S], TB [auth S], WA [auth R], X [auth Q]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth Q], AB [auth R], BA [auth Q], CA [auth Q], DA [auth Q], EA [auth Q], FA [auth Q], G [auth P], GA [auth Q], H [auth P], HA [auth Q], I [auth P], IA [auth Q], J [auth P], JA [auth Q], JB [auth S], K [auth P], KA [auth Q], KB [auth S], L [auth P], LA [auth Q], LB [auth S], M [auth P], MA [auth Q], MB [auth S], N [auth P], NA [auth Q], NB [auth S], O [auth P], OA [auth Q], OB [auth S], PB [auth S], QB [auth S], RB [auth S], XA [auth R], Y [auth Q], YA [auth R], Z [auth Q], ZA [auth R]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	FB [auth R], VB [auth S]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.132 
• R-Value Work: 0.082 
• R-Value Observed: 0.085 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.789	α = 90
b = 171.331	β = 121.55
c = 122.484	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-06-24 
Deposition Author(s): Wang, J., Lomkalin, I.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM022778

Revision History  

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary