5HJ1

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.222
R-Value Work: 0.192
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 11.71 kDa
Atom Count: 901
Modelled Residue Count: 97
Deposited Residue Count: 103
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VCA Query on VCA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	VACCENIC ACID C₁₈ H₃₄ O₂ UWHZIFQPPBDJPM-FPLPWBNLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.192
R-Value Observed: 0.193
Space Group: P 4₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M35HJ1

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Filippova, E.V.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-02-17
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.