6NLW | pdb_00006nlw

The crystal structure of class D carbapenem-hydrolyzing beta-lactamase BlaA from Shewanella oneidensis MR-1

PDB DOI: https://doi.org/10.2210/pdb6NLW/pdb

Classification: HYDROLASE
Organism(s): Shewanella oneidensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-01-09 Released: 2019-01-23
Deposition Author(s): Tan, K., Tesar, C., 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: 1.85 Å
R-Value Free:
0.225 (Depositor), 0.224 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of class D carbapenem-hydrolyzing beta-lactamase BlaA from Shewanella oneidensis MR-1

Tan, K., Tesar, C., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 117.42 kDa
Atom Count: 8,674
Modeled Residue Count: 970
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	246	Shewanella oneidensis	Mutation(s): 0 Gene Names: blaOXA-54 EC: 3.5.2.6
UniProt
Find proteins for Q6RFZ0 (Shewanella oneidensis) Explore Q6RFZ0 Go to UniProtKB: Q6RFZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6RFZ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain EA [auth B]	EA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Interactions & Density Focus chain EA [auth B]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain ZA [auth D] MOL2 format, chain ZA [auth D] mmCIF format, chain ZA [auth D]	ZA [auth D]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain ZA [auth D] Interactions & Density Focus chain ZA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain WA [auth D] SDF format, chain W [auth B] SDF format, chain VA [auth D] SDF format, chain V [auth B] SDF format, chain UA [auth D] SDF format, chain U [auth B] SDF format, chain TA [auth D] SDF format, chain T [auth B] SDF format, chain SA [auth D] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain PA [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain G [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A]	G [auth A] GA [auth C] H [auth A] HA [auth C] I [auth A] G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], L [auth A], M [auth A], PA [auth D], QA [auth D], RA [auth D], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain OA [auth D] SDF format, chain FA [auth C] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain FA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain FA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], FA [auth C], OA [auth D], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth C] Focus chain OA [auth D] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth C] Focus chain OA [auth D] Focus chain S [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain YA [auth D] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	CA [auth B] DA [auth B] MA [auth C] NA [auth C] O [auth A] CA [auth B], DA [auth B], MA [auth C], NA [auth C], O [auth A], P [auth A], Q [auth A], R [auth A], YA [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain YA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain YA [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain XA [auth D] SDF format, chain N [auth A] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] KA [auth C] LA [auth C] N [auth A] AA [auth B], BA [auth B], KA [auth C], LA [auth C], N [auth A], XA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain XA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain XA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.225 (Depositor), 0.224 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.333	α = 90
b = 61.391	β = 119.53
c = 122.802	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-23

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	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description