1G29 | pdb_00001g29

MALK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.247 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.203 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1G29

This is version 1.4 of the entry. See complete history

Literature

Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis.

Diederichs, K.Diez, J.Greller, G.Muller, C.Breed, J.Schnell, C.Vonrhein, C.Boos, W.Welte, W.

(2000) EMBO J 19: 5951-5961

  • DOI: https://doi.org/10.1093/emboj/19.22.5951
  • Primary Citation Related Structures: 
    1G29

  • PubMed Abstract: 

    The members of the ABC transporter family transport a wide variety of molecules into or out of cells and cellular compartments. Apart from a translocation pore, each member possesses two similar nucleoside triphosphate-binding subunits or domains in order to couple the energy-providing reaction with transport. In the maltose transporter of several Gram-negative bacteria and the archaeon Thermo coccus litoralis, the nucleoside triphosphate-binding subunit contains a C-terminal regulatory domain. A dimer of the subunit is attached cytoplasmically to the translocation pore. Here we report the crystal structure of this dimer showing two bound pyrophosphate molecules at 1.9 A resolution. The dimer forms by association of the ATPase domains, with the two regulatory domains attached at opposite poles. Significant deviation from 2-fold symmetry is seen at the interface of the dimer and in the regions corresponding to those residues known to be in contact with the translocation pore. The structure and its relationship to function are discussed in the light of known mutations from the homologous Escherichia coli and Salmonella typhimurium proteins.


  • Organizational Affiliation
    • Fachbereich Biologie, Universität Konstanz, M656, D-78457 Konstanz, Germany.

Macromolecule Content 

  • Total Structure Weight: 85.65 kDa 
  • Atom Count: 6,362 
  • Modeled Residue Count: 744 
  • Deposited Residue Count: 744 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MALTOSE TRANSPORT PROTEIN MALKA [auth 1],
B [auth 2]
372Thermococcus litoralisMutation(s): 0 
Gene Names: MALK
EC: 7.5.2.1
UniProt
Find proteins for Q9YGA6 (Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C))
Explore Q9YGA6 
Go to UniProtKB:  Q9YGA6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YGA6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POP

Query on POP



Download:Ideal Coordinates CCD File
AA [auth 1],
GB [auth 2]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
DIO

Query on DIO



Download:Ideal Coordinates CCD File
BA [auth 1],
CA [auth 1],
DA [auth 1]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AB [auth 2]
BB [auth 2]
D [auth 1]
E [auth 1]
EB [auth 2]
AB [auth 2],
BB [auth 2],
D [auth 1],
E [auth 1],
EB [auth 2],
HA [auth 2],
JA [auth 2],
K [auth 1],
MA [auth 2],
U [auth 1]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
GA [auth 2]
H [auth 1]
KA [auth 2]
N [auth 1]
QA [auth 2]
GA [auth 2],
H [auth 1],
KA [auth 2],
N [auth 1],
QA [auth 2],
RA [auth 2],
SA [auth 2],
UA [auth 2],
V [auth 1],
W [auth 1],
YA [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
CB [auth 2]
DB [auth 2]
F [auth 1]
FB [auth 2]
G [auth 1]
CB [auth 2],
DB [auth 2],
F [auth 1],
FB [auth 2],
G [auth 1],
I [auth 1],
IA [auth 2],
J [auth 1],
L [auth 1],
LA [auth 2],
M [auth 1],
NA [auth 2],
O [auth 1],
OA [auth 2],
P [auth 1],
PA [auth 2],
Q [auth 1],
R [auth 1],
S [auth 1],
T [auth 1],
TA [auth 2],
VA [auth 2],
WA [auth 2],
X [auth 1],
XA [auth 2],
Y [auth 1],
Z [auth 1],
ZA [auth 2]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
NH4

Query on NH4



Download:Ideal Coordinates CCD File
C [auth 1],
EA [auth 2],
FA [auth 2]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.247 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.203 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.718α = 90
b = 65.705β = 90
c = 77.912γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations