6AUF | pdb_00006auf

Crystal structure of Metalo beta Lactamases MIM-1 from Novosphingobium pentaromativorans

PDB DOI: https://doi.org/10.2210/pdb6AUF/pdb

Classification: HYDROLASE
Organism(s): Novosphingobium pentaromativorans US6-1
Expression System: Escherichia coli 042
Mutation(s): No

Deposited: 2017-08-31 Released: 2018-09-12
Deposition Author(s): Selleck, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.219 (Depositor), 0.222 (DCC)
R-Value Work:
0.173 (Depositor), 0.175 (DCC)
R-Value Observed:
0.177 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Metalo beta Lactamases MIM-1 from Novosphingobium pentaromativorans

Selleck, C.

To be published.

Macromolecule Content

Total Structure Weight: 32.2 kDa
Atom Count: 2,147
Modeled Residue Count: 273
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase-like protein	A [auth B]	300	Novosphingobium pentaromativorans US6-1	Mutation(s): 0 Gene Names: NSU_3853
UniProt
Find proteins for G6EHN2 (Novosphingobium pentaromativorans US6-1) Explore G6EHN2 Go to UniProtKB: G6EHN2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G6EHN2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B SDF format, chain C [auth B] MOL2 format, chain B MOL2 format, chain C [auth B] mmCIF format, chain B mmCIF format, chain C [auth B]	B, C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B Focus chain C [auth B] Interactions & Density Focus chain B Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.219 (Depositor), 0.222 (DCC)
R-Value Work: 0.173 (Depositor), 0.175 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.961	α = 90
b = 67.961	β = 90
c = 216.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-09-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-12
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Structure summary

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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.