6NI1 | pdb_00006ni1

Crystal Structure of the Beta Lactamase Class A penP from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb6NI1/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis subsp. subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-25 Released: 2019-01-30
Deposition Author(s): Kim, Y., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.156 (Depositor), 0.160 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Beta Lactamase Class A penP from Bacillus subtilis

Kim, Y., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 60.68 kDa
Atom Count: 4,535
Modeled Residue Count: 538
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	275	Bacillus subtilis subsp. subtilis	Mutation(s): 0 Gene Names: penP, S101441_02191 EC: 3.5.2.6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain I [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth B] G [auth B] H [auth B] D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.191 (Depositor), 0.190 (DCC)
R-Value Work: 0.156 (Depositor), 0.160 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.849	α = 90
b = 87.849	β = 90
c = 149.853	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary