6UAH

Crystal Structure of the Metallo-beta-Lactamase L1 from Stenotrophomonas maltophilia in the Complex with Hydrolyzed Meropenem

PDB DOI: https://doi.org/10.2210/pdb6UAH/pdb

Classification: HYDROLASE
Organism(s): Stenotrophomonas maltophilia K279a
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-10 Released: 2019-09-18
Deposition Author(s): Kim, Y., Maltseva, N., 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: 1.98 Å
R-Value Free: 0.203
R-Value Work: 0.173
R-Value Observed: 0.174

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Metallo-beta-Lactamase L1 from Stenotrophomonas maltophilia in the Complex with Hydrolyzed Meropenem

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

To be published.

Macromolecule Content

Total Structure Weight: 29.99 kDa
Atom Count: 2,224
Modelled Residue Count: 265
Deposited Residue Count: 275
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)	A	275	Stenotrophomonas maltophilia K279a	Mutation(s): 0 Gene Names: Smlt2667 EC: 3.5.2.6
UniProt
Find proteins for B2FTM1 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FTM1 Go to UniProtKB: B2FTM1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2FTM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMP (Subject of Investigation/LOI) Query on LMP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoy l)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid C₁₇ H₂₇ N₃ O₆ S CDYPSIIDXKMBLV-CFINEGTKSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.203
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.41	α = 90
b = 104.41	β = 90
c = 98.849	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-18

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: 2019-09-18
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.3: 2024-11-20
Changes: Structure summary