3SD9 | pdb_00003sd9

Crystal structure of serratia fonticola SFH-I: Source of the nucleophile in the catalytic mechanism of mono-zinc metallo-beta-lactamases

PDB DOI: https://doi.org/10.2210/pdb3SD9/pdb

Classification: HYDROLASE
Organism(s): Serratia fonticola
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-06-08 Released: 2011-07-13
Deposition Author(s): Fonseca, F., Saavedra, M.J., Correia, A., Spencer, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.213 (Depositor), 0.206 (DCC)
R-Value Work:
0.183 (Depositor)
R-Value Observed:
0.185 (Depositor)

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

Literature

Crystal Structure of Serratia fonticola Sfh-I: Activation of the Nucleophile in Mono-Zinc Metallo-beta-Lactamases

Fonseca, F., Bromley, E.H.C., Saavedra, M.J., Correia, A., Spencer, J.

To be published.

Macromolecule Content

Total Structure Weight: 52.72 kDa
Atom Count: 3,930
Modeled Residue Count: 459
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	233	Serratia fonticola	Mutation(s): 0 Gene Names: blaSfh-I, sfhI EC: 3.5.2.6
UniProt
Find proteins for Q9RMI1 (Serratia fonticola) Explore Q9RMI1 Go to UniProtKB: Q9RMI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RMI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.213 (Depositor), 0.206 (DCC)
R-Value Work: 0.183 (Depositor)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.965	α = 90
b = 86.412	β = 90.07
c = 72.193	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-07-13
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.