5HJ1 | pdb_00005hj1

Crystal structure of PDZ domain of pullulanase C protein of type II secretion system from Klebsiella pneumoniae in complex with fatty acid

• PDB DOI: https://doi.org/10.2210/pdb5HJ1/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-12 Released: 2016-02-17 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.222 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of PDZ domain of pullulanase C protein of type II secretion system from Klebsiella pneumoniae in complex with fatty acid

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 11.71 kDa 
• Atom Count: 901 
• Modeled Residue Count: 97 
• Deposited Residue Count: 103 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pullulanase C protein	A	103	Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044	Mutation(s): 0  Gene Names: YP_002917874

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VCA	B [auth A]	VACCENIC ACID C18 H34 O2 UWHZIFQPPBDJPM-FPLPWBNLSA-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: 1.50 Å
• R-Value Free:  0.222 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35hj1

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.636	α = 90
b = 47.636	β = 90
c = 93.202	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data scaling
HKL-3000	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary