5BV2 | pdb_00005bv2

Crystal structure of E. coli HPII catalase variant

  • 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)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.132 (Depositor), 0.132 (DCC) 
  • R-Value Work: 
    0.082 (Depositor), 0.082 (DCC) 
  • R-Value Observed: 
    0.085 (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 1.4 of the entry. See complete history. 

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.

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Catalase HPIIA [auth P],
B [auth Q],
C [auth R],
D [auth S]		753Escherichia coliMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for P21179 (Escherichia coli (strain K12))
Explore P21179 
Go to UniProtKB:  P21179
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21179
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HDD

Query on HDD


Download:Ideal Coordinates CCD File
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

Query on PG4


Download:Ideal Coordinates CCD File
GB [auth R]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE


Download:Ideal Coordinates CCD File
BB [auth R],
CB [auth R],
P		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG


Download:Ideal Coordinates CCD File
R [auth P]
RA [auth Q]
S [auth P]
SA [auth Q]
T [auth P]
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

Query on SO4


Download:Ideal Coordinates CCD File
UB [auth S],
V [auth P]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL


Download:Ideal Coordinates CCD File
DB [auth R]
EB [auth R]
F [auth P]
IB [auth S]
PA [auth Q]
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

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth Q]
AB [auth R]
BA [auth Q]
CA [auth Q]
DA [auth Q]
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

Query on MG


Download:Ideal Coordinates CCD File
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 (Depositor), 0.132 (DCC) 
  • R-Value Work:  0.082 (Depositor), 0.082 (DCC) 
  • R-Value Observed: 0.085 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.789α = 90
b = 171.331β = 121.55
c = 122.484γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM022778

Revision History  (Full details and data files)

  • 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