3SJN

Crystal structure of enolase Spea_3858 (target EFI-500646) from Shewanella pealeana with magnesium bound

PDB DOI: https://doi.org/10.2210/pdb3SJN/pdb

Classification: LYASE
Organism(s): Shewanella pealeana ATCC 700345
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-06-21 Released: 2011-07-06
Deposition Author(s): Patskovsky, Y., Kim, J., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., 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: 1.90 Å
R-Value Free: 0.176
R-Value Work: 0.160
R-Value Observed: 0.161

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Enolase Spea_3858 from Shewanella Pealeana

Patskovsky, Y., Kim, J., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 82.56 kDa
Atom Count: 6,121
Modelled Residue Count: 746
Deposited Residue Count: 748
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 protein	A, B	374	Shewanella pealeana ATCC 700345	Mutation(s): 0 Gene Names: Spea_3858
UniProt
Find proteins for A8H9D1 (Shewanella pealeana (strain ATCC 700345 / ANG-SQ1)) Explore A8H9D1 Go to UniProtKB: A8H9D1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8H9D1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
UNL Query on UNL Download Ideal Coordinates CCD File	D [auth A], G [auth B]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.176
R-Value Work: 0.160
R-Value Observed: 0.161
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.207	α = 90
b = 109.207	β = 90
c = 141.034	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-06

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-07-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-08-03
Changes: Structure summary
Version 1.3: 2012-02-22
Changes: Other, Structure summary
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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3SJN

Crystal structure of enolase Spea_3858 (target EFI-500646) from Shewanella pealeana with magnesium bound

Crystal Structure of Enolase Spea_3858 from Shewanella Pealeana

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)