4GIR | pdb_00004gir

Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, ethylene glycol and sulfate bound (ordered loops, space group P41212)

PDB DOI: https://doi.org/10.2210/pdb4GIR/pdb

Classification: LYASE
Organism(s): Vibrio harveyi 1DA3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-08 Released: 2012-08-29
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.193 (Depositor), 0.191 (DCC)
R-Value Work:
0.148 (Depositor), 0.147 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, ethylene glycol and sulfate bound (ordered loops, space group P41212)

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 194.03 kDa
Atom Count: 14,452
Modeled Residue Count: 1,613
Deposited Residue Count: 1,688
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase	A, B, C, D	422	Vibrio harveyi 1DA3	Mutation(s): 0 Gene Names: VME_00770
UniProt
Find proteins for D0X4R4 (Vibrio harveyi (strain 1DA3)) Explore D0X4R4 Go to UniProtKB: D0X4R4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0X4R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B], S [auth C], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain W [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain AA [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth D]	AA [auth D], I [auth A], O [auth B], U [auth C], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Y [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [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 Z [auth D] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [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 Z [auth D] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [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] P [auth B] G [auth A], H [auth A], M [auth B], N [auth B], P [auth B], Q [auth B], T [auth C], X [auth D], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain X [auth D] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain X [auth D] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], R [auth C], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain V [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.193 (Depositor), 0.191 (DCC)
R-Value Work: 0.148 (Depositor), 0.147 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.836	α = 90
b = 146.836	β = 90
c = 169.524	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description