3SBF | pdb_00003sbf

Crystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES BACTERIUM complexed with Mg and D-Arabinonate

PDB DOI: https://doi.org/10.2210/pdb3SBF/pdb

Classification: ISOMERASE
Organism(s): Vibrionales bacterium SWAT-3
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-06-04 Released: 2012-06-06
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.206 (Depositor), 0.200 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the mutant P311A of enolase superfamily member from Vibrionales bacterium complexed with Mg and D-Arabinonate

Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 182.78 kDa
Atom Count: 14,132
Modeled Residue Count: 1,583
Deposited Residue Count: 1,604
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mandelate racemase / muconate lactonizing enzyme	A, B, C, D	401	Vibrionales bacterium SWAT-3	Mutation(s): 1 Gene Names: VSWAT3_13707
UniProt
Find proteins for A5KUH4 (Vibrionales bacterium (strain SWAT-3)) Explore A5KUH4 Go to UniProtKB: A5KUH4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5KUH4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain F [auth A]	F [auth A], L [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth C]
D8T Query on D8T Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], O [auth D]	D-arabinonic acid C₅ H₁₀ O₆ QXKAIJAYHKCRRA-JJYYJPOSSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.206 (Depositor), 0.200 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.372	α = 90
b = 163.372	β = 90
c = 110.412	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

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Crystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES BACTERIUM complexed with Mg and D-Arabinonate

Crystal structure of the mutant P311A of enolase superfamily member from Vibrionales bacterium complexed with Mg and D-Arabinonate

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations