4GFI | pdb_00004gfi

Crystal structure of EFI-502318, an enolase family member from Agrobacterium tumefaciens with homology to dipeptide epimerases (bound sodium, L-Ala-L-Glu with ordered loop)

PDB DOI: https://doi.org/10.2210/pdb4GFI/pdb

Classification: ISOMERASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-03 Released: 2012-08-29
Deposition Author(s): Vetting, M.W., Bouvier, J.T., Morisco, L.L., Wasserman, S.R., Sojitra, S., 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:
0.213 (Depositor), 0.212 (DCC)
R-Value Work:
0.171 (Depositor), 0.173 (DCC)
R-Value Observed:
0.173 (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 EFI-502318, an enolase family member from Agrobacterium tumefaciens with homology to dipeptide epimerases (bound sodium, l-ala-l-glu with ordered loop)

Vetting, M.W., Bouvier, J.T., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 142.92 kDa
Atom Count: 10,668
Modeled Residue Count: 1,304
Deposited Residue Count: 1,316
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, D	329	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: Atu1648 EC: 5.1.1
UniProt
Find proteins for A9CIT6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CIT6 Go to UniProtKB: A9CIT6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9CIT6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU Query on GLU Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], R [auth C], W [auth D]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain W [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B], N [auth B], T [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], Q [auth C], V [auth D]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain Q [auth C] Focus chain V [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain S [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B]	K [auth B], L [auth B], S [auth C], X [auth D], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], P [auth C], U [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.213 (Depositor), 0.212 (DCC)
R-Value Work: 0.171 (Depositor), 0.173 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.901	α = 90
b = 77.274	β = 90
c = 215.825	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