3M0Z | pdb_00003m0z

Crystal structure of putative aldolase from Klebsiella pneumoniae.

• PDB DOI: https://doi.org/10.2210/pdb3M0Z/pdb

• Classification: LYASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-03 Released: 2010-03-31 
• Deposition Author(s): Chang, C., Rakowski, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.155 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.129 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Literature

Crystal structure of putative aldolase from Klebsiella pneumoniae.

Chang, C., Rakowski, E., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 107.65 kDa 
• Atom Count: 9,617 
• Modeled Residue Count: 992 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative aldolase	A, B, C, D	249	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: KPN78578_45670, KPN_04640
UniProt
Find proteins for A6THF7 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6THF7  Go to UniProtKB:  A6THF7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	I [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	E [auth A], F [auth B], H [auth C], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.155 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.129 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.955	α = 90
b = 80.073	β = 94.11
c = 80.911	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Chang, C., Rakowski, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary