4PEM | pdb_00004pem

Crystal Structure of S1G mutant of Penicillin G Acylase from Kluyvera citrophila

PDB DOI: https://doi.org/10.2210/pdb4PEM/pdb

Classification: HYDROLASE
Organism(s): Kluyvera cryocrescens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2014-04-24 Released: 2015-07-22
Deposition Author(s): Ramasamy, S., Varshney, N.K., Brannigan, J.A., Wilkinson, A.J., Suresh, C.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.292 (Depositor), 0.290 (DCC)
R-Value Work:
0.248 (Depositor), 0.251 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of S1G mutant of Penicillin G Acylase from Kluyvera citrophilla

Varshney, N.K., Ramasamy, S., Brannigan, J.A., Wilkinson, A.J., Suresh, C.G.

To be published.

Macromolecule Content

Total Structure Weight: 379.84 kDa
Atom Count: 25,838
Modeled Residue Count: 3,238
Deposited Residue Count: 3,416
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin G acylase Alpha	A, C, E, G	286	Kluyvera cryocrescens	Mutation(s): 0
UniProt
Find proteins for A0A068F6N5 (Kluyvera cryocrescens) Explore A0A068F6N5 Go to UniProtKB: A0A068F6N5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A068F6N5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin G acylase Beta	B, D, F, H	568	Kluyvera cryocrescens	Mutation(s): 1
UniProt
Find proteins for A0A068F6N5 (Kluyvera cryocrescens) Explore A0A068F6N5 Go to UniProtKB: A0A068F6N5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A068F6N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.292 (Depositor), 0.290 (DCC)
R-Value Work: 0.248 (Depositor), 0.251 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54	α = 104.05
b = 124.561	β = 101.37
c = 135.139	γ = 96.51

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
XDS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-07-22

Deposition Author(s):

Brannigan, J.A.

Wilkinson, A.J.

Revision History (Full details and data files)

Version 1.0: 2015-07-22
Type: Initial release
Version 1.1: 2023-09-27
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy

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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.