9BI7 | pdb_00009bi7

YqiA, Klebsiella pneumoniae serine hydrolase, unbound

PDB DOI: https://doi.org/10.2210/pdb9BI7/pdb

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

Deposited: 2024-04-22 Released: 2025-05-07
Deposition Author(s): Randall, G.T., Fellner, M.
Funding Organization(s): MBIE China-MWC Collaboration

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.213 (Depositor), 0.212 (DCC)
R-Value Work:
0.175 (Depositor), 0.173 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

YqiA, Klebsiella pneumoniae serine hydrolase, unbound

Randall, G.T., Fellner, M.

To be published.

Macromolecule Content

Total Structure Weight: 21.82 kDa
Atom Count: 1,651
Modeled Residue Count: 192
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A	194	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: yqiA, B5L96_16095, B6I68_11455, BANRA_00684, BB784_03840, BL124_00019630, CK244_014295, DL426_23790, DW281_23375, EAO17_10155... yqiA, B5L96_16095, B6I68_11455, BANRA_00684, BB784_03840, BL124_00019630, CK244_014295, DL426_23790, DW281_23375, EAO17_10155, FXN67_07320, G4V31_19105, G7Z27_03770, GJJ08_003500, GJJ13_003365, GJJ18_06885, GNF00_15605, GS419_03475, HJX03_03495, NCTC11679_00755, NCTC13443_06427, NCTC13635_02885, NCTC5047_02742, NCTC5052_03996, NCTC8849_05396, NCTC9601_00008, NCTC9637_01258, NCTC9645_02747, NCTC9661_01486, QIG75_16940, SAMEA3499874_00665, SAMEA3499901_04234, SAMEA3512100_04022, SAMEA3515122_03433, SAMEA3538658_02075, SAMEA3538828_03988, SAMEA3720909_03528, SAMEA4364603_00807, SAMEA4370542_02038, SAMEA4873597_05118, SAMEA4873632_04098, VKR_00711
UniProt
Find proteins for A0A0W8AWE3 (Klebsiella pneumoniae) Explore A0A0W8AWE3 Go to UniProtKB: A0A0W8AWE3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0W8AWE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.213 (Depositor), 0.212 (DCC)
R-Value Work: 0.175 (Depositor), 0.173 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.459	α = 90
b = 62.459	β = 90
c = 80.361	γ = 120

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: 2025-05-07

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: 2025-05-07
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.