6V3U

Crystal Structure of the NDM_FIM-1 like Metallo-beta-Lactamase from Erythrobacter litoralis in the Mono-Zinc Form

PDB DOI: https://doi.org/10.2210/pdb6V3U/pdb

Classification: HYDROLASE
Organism(s): Erythrobacter litoralis HTCC2594
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-26 Released: 2020-01-15
Deposition Author(s): Kim, Y., Maltseva, N., Mulligan, R., 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: 2.00 Å
R-Value Free: 0.238
R-Value Work: 0.202
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the NDM_FIM-1 like Metallo-beta-Lactamase from Erythrobacter litoralis in the Mono-Zinc Form

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

To be published.

Macromolecule Content

Total Structure Weight: 52.76 kDa
Atom Count: 3,355
Modelled Residue Count: 430
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase II	A, B	242	Erythrobacter litoralis HTCC2594	Mutation(s): 0 Gene Names: ELI_07580
UniProt
Find proteins for Q2N9N3 (Erythrobacter litoralis (strain HTCC2594)) Explore Q2N9N3 Go to UniProtKB: Q2N9N3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N9N3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	F [auth A], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
OCS Query on OCS	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.238
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.043	α = 90
b = 80.043	β = 90
c = 72.502	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-01-15

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: 2020-01-15
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description

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6V3U

Crystal Structure of the NDM_FIM-1 like Metallo-beta-Lactamase from Erythrobacter litoralis in the Mono-Zinc Form

Crystal Structure of the NDM_FIM-1 like Metallo-beta-Lactamase from Erythrobacter litoralis in the Mono-Zinc Form

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)