6WYX

Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 5.0

PDB DOI: https://doi.org/10.2210/pdb6WYX/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-13 Released: 2020-10-14
Deposition Author(s): Strzelczyk, P., Zhang, D., Wlodawer, A., Lubkowski, J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 ?
R-Value Free: 0.120
R-Value Work: 0.088
R-Value Observed: 0.088

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Generalized enzymatic mechanism of catalysis by tetrameric L-asparaginases from mesophilic bacteria.

Strzelczyk, P., Zhang, D., Dyba, M., Wlodawer, A., Lubkowski, J.

(2020) Sci Rep 10: 17516

DOI: https://doi.org/10.1038/s41598-020-74480-4

Macromolecule Content

Total Structure Weight: 145.41 kDa
Atom Count: 10,945
Modelled Residue Count: 1,273
Deposited Residue Count: 1,348
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaminase-asparaginase	A, B, C, D	337	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: ansB, PP_2453 EC: 3.5.1.38
UniProt
Find proteins for Q88K39 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88K39 Go to UniProtKB: Q88K39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88K39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASP (Subject of Investigation/LOI) Query on ASP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth D] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth D] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C]	E [auth A], F [auth B], H [auth C], I [auth D]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 ?
R-Value Free: 0.120
R-Value Work: 0.088
R-Value Observed: 0.088
Space Group: P 3₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 80.958	α = 90
b = 80.958	β = 90
c = 176.819	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 1.1: 2020-10-21
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description

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6WYX

Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 5.0

Generalized enzymatic mechanism of catalysis by tetrameric L-asparaginases from mesophilic bacteria.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)