6V5F | pdb_00006v5f

L-asparaginase from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb6V5F/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 2019-12-04 Released: 2021-02-03
Deposition Author(s): Souza, T.A.C.B., Morais, S.B., Morini, F.S., Meissner, G.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.298 (Depositor), 0.297 (DCC)
R-Value Work:
0.230 (Depositor), 0.231 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

L-asparaginase from Escherichia coli: Novel insights about the behavior of flexible part of the active site

Souza, T.A.C.B., Morais, S.B., Morini, F.S., Meissner, G.O.

To be published.

Macromolecule Content

Total Structure Weight: 139.01 kDa
Atom Count: 9,423
Modeled Residue Count: 1,227
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase 2	A, B, C, D	326	Escherichia coli	Mutation(s): 0 EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12)) Explore P00805 Go to UniProtKB: P00805
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00805
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 H [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain E [auth A]	E [auth A], H [auth D]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth D]
SIN (Subject of Investigation/LOI) Query on SIN Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B]	F [auth B], G [auth C]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain F [auth B] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.298 (Depositor), 0.297 (DCC)
R-Value Work: 0.230 (Depositor), 0.231 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.917	α = 90
b = 125.435	β = 106.94
c = 68.816	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-03
Type: Initial release
Version 1.1: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

6V5F | pdb_00006v5f

L-asparaginase from Escherichia coli

Literature

L-asparaginase from Escherichia coli: Novel insights about the behavior of flexible part of the active site

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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