5X9I | pdb_00005x9i

Unique Choloylglycine Hydrolase(CGH) member Mutant (C1S) from Shewanella loihica PV-4

PDB DOI: https://doi.org/10.2210/pdb5X9I/pdb

Classification: HYDROLASE
Organism(s): Shewanella loihica PV-4
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-03-07 Released: 2018-03-07
Deposition Author(s): Ramasamy, S., Philem, P., Yadav, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.208 (Depositor), 0.207 (DCC)
R-Value Work:
0.185 (Depositor), 0.184 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Unique Choloylglycine Hydrolase(CGH) member from Shewanella loihica PV-4

Philem, P., Yadav, Y., Prabune, A.A., Ramasamy, S.

To be published.

Macromolecule Content

Total Structure Weight: 76.36 kDa
Atom Count: 5,512
Modeled Residue Count: 666
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin V acylase-like protein	A, B	339	Shewanella loihica PV-4	Mutation(s): 1 Gene Names: Shew_0681 EC: 3.5.1.24
UniProt
Find proteins for A3QAQ5 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QAQ5 Go to UniProtKB: A3QAQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3QAQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OOA Query on OOA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	3-OXOOCTANOIC ACID C₈ H₁₄ O₃ FWNRRWJFOZIGQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.208 (Depositor), 0.207 (DCC)
R-Value Work: 0.185 (Depositor), 0.184 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.788	α = 90
b = 52.42	β = 115.96
c = 99.205	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.