3PMM | pdb_00003pmm

The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

• PDB DOI: https://doi.org/10.2210/pdb3PMM/pdb

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


• Deposited: 2010-11-17 Released: 2010-12-29 
• Deposition Author(s): Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 45.32 kDa 
• Atom Count: 3,509 
• Modeled Residue Count: 381 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cytoplasmic protein	A	382	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: KPN78578_23540, KPN_02389
UniProt
Find proteins for A6TB44 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TB44  Go to UniProtKB:  A6TB44

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	B [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
FMT	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.085	α = 90
b = 143.085	β = 90
c = 129.612	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2012-08-08
  Changes: Other
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary