4BGU | pdb_00004bgu

1.50 A resolution structure of the malate dehydrogenase from Haloferax volcanii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.179 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4BGU

This is version 1.2 of the entry. See complete history. 

Literature

Insight Into Structural Evolution of Extremophilic Proteins

Talon, R., Girard, E., Franzetti, B., Zaccai, G., Madern, D.

To be published.

Macromolecule Content 

  • Total Structure Weight: 135.51 kDa 
  • Atom Count: 11,435 
  • Modeled Residue Count: 1,212 
  • Deposited Residue Count: 1,212 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MALATE DEHYDROGENASE
A, B, C, D
303Haloferax volcaniiMutation(s): 0 
EC: 1.1.1.37
UniProt
Find proteins for Q9P9L2 (Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2))
Explore Q9P9L2 
Go to UniProtKB:  Q9P9L2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P9L2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33

Query on P33


Download:Ideal Coordinates CCD File
HA [auth A]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
1PE

Query on 1PE


Download:Ideal Coordinates CCD File
FB [auth B],
GA [auth A]		PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4

Query on PG4


Download:Ideal Coordinates CCD File
CC [auth C],
DC [auth C]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE


Download:Ideal Coordinates CCD File
DD [auth D],
EB [auth B],
FA [auth A]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS

Query on TRS


Download:Ideal Coordinates CCD File
DB [auth B],
EA [auth A]		2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
K

Query on K


Download:Ideal Coordinates CCD File
E [auth A]
EC [auth D]
F [auth A]
FC [auth D]
G [auth A]
E [auth A],
EC [auth D],
F [auth A],
FC [auth D],
G [auth A],
GB [auth C],
GC [auth D],
H [auth A],
HB [auth C],
HC [auth D],
I [auth A],
IA [auth B],
IB [auth C],
IC [auth D],
J [auth A],
JA [auth B],
JB [auth C],
K [auth A],
KA [auth B],
KB [auth C],
LA [auth B],
LB [auth C],
MB [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth B]
AC [auth C]
AD [auth D]
BA [auth A]
AA [auth A],
AB [auth B],
AC [auth C],
AD [auth D],
BA [auth A],
BB [auth B],
BC [auth C],
BD [auth D],
CA [auth A],
CB [auth B],
CD [auth D],
DA [auth A],
JC [auth D],
KC [auth D],
L [auth A],
LC [auth D],
M [auth A],
MA [auth B],
MC [auth D],
N [auth A],
NA [auth B],
NB [auth C],
NC [auth D],
O [auth A],
OA [auth B],
OB [auth C],
OC [auth D],
P [auth A],
PA [auth B],
PB [auth C],
PC [auth D],
Q [auth A],
QA [auth B],
QB [auth C],
QC [auth D],
R [auth A],
RA [auth B],
RB [auth C],
RC [auth D],
S [auth A],
SA [auth B],
SB [auth C],
SC [auth D],
T [auth A],
TA [auth B],
TB [auth C],
TC [auth D],
U [auth A],
UA [auth B],
UB [auth C],
UC [auth D],
V [auth A],
VA [auth B],
VB [auth C],
VC [auth D],
W [auth A],
WA [auth B],
WB [auth C],
WC [auth D],
X [auth A],
XA [auth B],
XB [auth C],
XC [auth D],
Y [auth A],
YA [auth B],
YB [auth C],
YC [auth D],
Z [auth A],
ZA [auth B],
ZB [auth C],
ZC [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.76α = 90
b = 82.319β = 101.72
c = 112.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary