3PG4 | pdb_00003pg4

The crystal structure of New Delhi Metallo-beta lactamase (NDM-1)

PDB DOI: https://doi.org/10.2210/pdb3PG4/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-10-29 Released: 2011-11-16
Deposition Author(s): Kim, H.T., Cho, Y.S., Chang, H.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.237 (Depositor), 0.238 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.202 (Depositor)

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

Literature

The crystal structure of New Delhi Metallo-beta lactamase (NDM-1)

Kim, H.T., Cho, Y.S., Chang, H.J.

To be published.

Macromolecule Content

Total Structure Weight: 24.43 kDa
Atom Count: 1,852
Modeled Residue Count: 230
Deposited Residue Count: 230
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase	A	230	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bla NDM-1, blaNDM-1 EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422 Go to UniProtKB: C7C422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7C422
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.237 (Depositor), 0.238 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.539	α = 90
b = 77.539	β = 90
c = 177.74	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-16
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, 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.