5ZR8

Crystal Structure Of NDM-1 Metallo-beta-lactamase

PDB DOI: https://doi.org/10.2210/pdb5ZR8/pdb

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

Deposited: 2018-04-23 Released: 2019-04-24
Deposition Author(s): Wachino, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.168
R-Value Work: 0.146
R-Value Observed: 0.147

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure Of NDM-1 Metallo-beta-lactamase

Wachino, J.

To be published.

Macromolecule Content

Total Structure Weight: 52.77 kDa
Atom Count: 4,000
Modelled Residue Count: 460
Deposited Residue Count: 492
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 [auth E]	246	Escherichia coli	Mutation(s): 0 Gene Names: blaNDM-1, bla NDM-1, AM434_27040, APU18_05360, AZ95_0035, BET08_16280, BVL39_26630, CA268_28970, ECS01_0033, MS6198_A142... blaNDM-1, bla NDM-1, AM434_27040, APU18_05360, AZ95_0035, BET08_16280, BVL39_26630, CA268_28970, ECS01_0033, MS6198_A142, NDM1Dok01_N0175, pNDM102337_147, pNDM10505_149 EC: 3.5.2.6
UniProt
Find proteins for E5KIY2 (Escherichia coli) Explore E5KIY2 Go to UniProtKB: E5KIY2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E5KIY2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain K [auth E] SDF format, chain J [auth E] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth E] MOL2 format, chain J [auth E] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth E] mmCIF format, chain J [auth E]	C [auth A] D [auth A] E [auth A] I [auth A] J [auth E] C [auth A], D [auth A], E [auth A], I [auth A], J [auth E], K [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth E] Focus chain K [auth E] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth E] Focus chain K [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.168
R-Value Work: 0.146
R-Value Observed: 0.147
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.08	α = 90
b = 73.9	β = 90
c = 77.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

Wachino, J.

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description