4BGU

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 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • 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

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FB [auth B],
GA [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

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CC [auth C],
DC [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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DD [auth D],
EB [auth B],
FA [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS
Query on TRS

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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 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • 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



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