3THU | pdb_00003thu

Crystal structure of an enolase from sphingomonas sp. ska58 (efi target efi-501683) with bound mg

PDB DOI: https://doi.org/10.2210/pdb3THU/pdb

Classification: LYASE
Organism(s): Sphingomonas sp. SKA58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-19 Released: 2011-09-14
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.165 (Depositor), 0.162 (DCC)
R-Value Work:
0.138 (Depositor), 0.135 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of an enolase from sphingomonas sp. ska58 (efi target efi-501683) with bound mg

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

To be published.

Macromolecule Content

Total Structure Weight: 144 kDa
Atom Count: 10,853
Modeled Residue Count: 1,213
Deposited Residue Count: 1,278
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase / muconate lactonizing enzyme family protein	A, B, C	426	Sphingomonas sp. SKA58	Mutation(s): 0 Gene Names: SKA58_08619 EC: 4.2.1.8
UniProt
Find proteins for Q1NAJ2 (Sphingomonas sp. (strain SKA58)) Explore Q1NAJ2 Go to UniProtKB: Q1NAJ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1NAJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] L [auth B] M [auth B] N [auth B] F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain Q [auth C]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] O [auth B] P [auth B] U [auth C] H [auth A], I [auth A], O [auth B], P [auth B], U [auth C], V [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.165 (Depositor), 0.162 (DCC)
R-Value Work: 0.138 (Depositor), 0.135 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.799	α = 90
b = 124.799	β = 90
c = 343.092	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-09-14

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-09-14
Type: Initial release
Version 1.1: 2012-02-22
Changes: Structure summary
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description