6L3S | pdb_00006l3s

Crystal structure of metallo-beta-lactamase IMP-27 from Morganella morganii

PDB DOI: https://doi.org/10.2210/pdb6L3S/pdb

Classification: HYDROLASE
Organism(s): Morganella morganii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-10-15 Released: 2020-10-28
Deposition Author(s): Kato, Y., Shimizu-Ibuka, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.200 (Depositor), 0.207 (DCC)
R-Value Work:
0.178 (Depositor), 0.189 (DCC)
R-Value Observed:
0.179 (Depositor)

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

Literature

Crystal structure of the metallo-beta-lactamase IMP-27

Kato, Y., Shimizu-Ibuka, A.

To be published.

Macromolecule Content

Total Structure Weight: 51.14 kDa
Atom Count: 3,758
Modeled Residue Count: 436
Deposited Residue Count: 458
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMP-27 metallo-beta-lactamase	A, B	229	Morganella morganii	Mutation(s): 0 Gene Names: blaIMP-27 EC: 3.5.2.6
UniProt
Find proteins for A0A286S0G7 (Morganella morganii) Explore A0A286S0G7 Go to UniProtKB: A0A286S0G7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A286S0G7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) 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 B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.200 (Depositor), 0.207 (DCC)
R-Value Work: 0.178 (Depositor), 0.189 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.59	α = 90
b = 71.25	β = 90
c = 136.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-10-28

Deposition Author(s):

Shimizu-Ibuka, A.

Revision History (Full details and data files)

Version 1.0: 2020-10-28
Type: Initial release
Version 1.1: 2023-11-22
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.