6PBL | pdb_00006pbl

Crystal structure of Malate dehydrogenase from Legionella pneumophila Philadelphia 1

• PDB DOI: https://doi.org/10.2210/pdb6PBL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-06-14 Released: 2019-07-24 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of Malate dehydrogenase from Legionella pneumophila Philadelphia 1

Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 74.15 kDa 
• Atom Count: 5,685 
• Modeled Residue Count: 654 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	338	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: mdh, lpg2352 EC: 1.1.1.37
UniProt
Find proteins for Q5ZT13 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZT13  Go to UniProtKB:  Q5ZT13

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36pbl

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.56	α = 90
b = 79.79	β = 90
c = 152.47	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description