6X9Y | pdb_00006x9y

The crystal structure of a Beta-lactamase from Escherichia coli CFT073

PDB DOI: https://doi.org/10.2210/pdb6X9Y/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli CFT073
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-03 Released: 2020-06-17
Deposition Author(s): Tan, K., Wu, R., 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: 1.90 Å
R-Value Free:
0.198 (Depositor), 0.199 (DCC)
R-Value Work:
0.161 (Depositor), 0.162 (DCC)
R-Value Observed:
0.162 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

The crystal structure of a Beta-lactamase from Escherichia coli CFT073

Tan, K., Wu, R., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 80.99 kDa
Atom Count: 5,907
Modeled Residue Count: 717
Deposited Residue Count: 722
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	361	Escherichia coli CFT073	Mutation(s): 0 Gene Names: ampC, c5238 EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12)) Explore P00811 Go to UniProtKB: P00811
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00811
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRT Query on SRT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], M [auth B], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] I [auth B] C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.198 (Depositor), 0.199 (DCC)
R-Value Work: 0.161 (Depositor), 0.162 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.176	α = 90
b = 128.176	β = 90
c = 92.761	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-17

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: 2020-06-17
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references

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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.