5EVI | pdb_00005evi

Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae

PDB DOI: https://doi.org/10.2210/pdb5EVI/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas syringae pv. tomato str. DC3000
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-11-19 Released: 2016-01-13
Deposition Author(s): Kim, Y., Hatzos-Skintges, C., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.163 (Depositor), 0.170 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae

Kim, Y., Hatzos-Skintges, C., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 163.82 kDa
Atom Count: 11,790
Modeled Residue Count: 1,430
Deposited Residue Count: 1,464
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-Lactamase/D-Alanine Carboxypeptidase	A	366	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0 Gene Names: ampC, PSPTO_3594 EC: 3.5.2.6
UniProt
Find proteins for Q87Z37 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q87Z37 Go to UniProtKB: Q87Z37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87Z37
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-Lactamase/D-Alanine Carboxypeptidase	B	366	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0 Gene Names: ampC, PSPTO_3594 EC: 3.5.2.6
UniProt
Find proteins for Q87Z37 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q87Z37 Go to UniProtKB: Q87Z37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87Z37
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-Lactamase/D-Alanine Carboxypeptidase	C	366	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0 Gene Names: ampC, PSPTO_3594 EC: 3.5.2.6
UniProt
Find proteins for Q87Z37 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q87Z37 Go to UniProtKB: Q87Z37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87Z37
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-Lactamase/D-Alanine Carboxypeptidase	D	366	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0 Gene Names: ampC, PSPTO_3594 EC: 3.5.2.6
UniProt
Find proteins for Q87Z37 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q87Z37 Go to UniProtKB: Q87Z37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87Z37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	E [auth A] F [auth A] H [auth B] J [auth C] K [auth C] E [auth A], F [auth A], H [auth B], J [auth C], K [auth C], O [auth D], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain O [auth D] Focus chain P [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	G [auth A] I [auth B] L [auth C] M [auth C] N [auth C] G [auth A], I [auth B], L [auth C], M [auth C], N [auth C], Q [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.163 (Depositor), 0.170 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.869	α = 89.94
b = 72.645	β = 90.01
c = 93.77	γ = 90.08

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2019-12-04
Changes: Author supporting evidence, Data collection, Derived calculations
Version 1.2: 2025-04-02
Changes: Data collection, Database references, Structure summary

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Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae

Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae

Entity ID: 1

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

5EVI | pdb_00005evi