9BD4 | pdb_00009bd4

YjfP, Klebsiella pneumoniae serine hydrolase, unbound

PDB DOI: https://doi.org/10.2210/pdb9BD4/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-11 Released: 2025-04-30
Deposition Author(s): Randall, G.T., Fellner, M.
Funding Organization(s): MBIE China-MWC Collaboration

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.161 (Depositor), 0.162 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Klebsiella pneumoniae Serine Hydrolase

Randall, G.T.

To be published.

Macromolecule Content

Total Structure Weight: 53.67 kDa
Atom Count: 4,193
Modeled Residue Count: 479
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B	242	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: CK244_008325, NCTC13465_04963, NCTC5052_05330, NCTC9601_05351, NCTC9617_04952, NCTC9645_01577, NCTC9661_05640, SAMEA3512100_04172, SAMEA4873632_04766 EC: 3.1.1.23
UniProt
Find proteins for A0A060VRI4 (Klebsiella pneumoniae) Explore A0A060VRI4 Go to UniProtKB: A0A060VRI4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A060VRI4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.175 (Depositor), 0.175 (DCC)
R-Value Work: 0.161 (Depositor), 0.162 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.706	α = 90
b = 68.195	β = 77.16
c = 65.363	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
MBIE China-MWC Collaboration	New Zealand	Nr.3720870

Revision History (Full details and data files)

Version 1.0: 2025-04-30
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.