4DX3 | pdb_00004dx3

Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502086) from Agrobacterium tumefaciens, with a succinimide residue

PDB DOI: https://doi.org/10.2210/pdb4DX3/pdb

Classification: ISOMERASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-02-27 Released: 2012-04-18
Deposition Author(s): Vetting, M.W., Bouvier, J.T., Toro, R., Bhosle, R., Al Obaidi, N.F., 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: 1.65 Å
R-Value Free:
0.172 (Depositor), 0.173 (DCC)
R-Value Work:
0.153 (Depositor), 0.153 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502086) from Agrobacterium tumefaciens, with a succinimide residue

Vetting, M.W., Bouvier, J.T., Toro, R., Bhosle, R., Al Obaidi, N.F., 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: 44.2 kDa
Atom Count: 3,208
Modeled Residue Count: 361
Deposited Residue Count: 400
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	400	Agrobacterium fabrum str. C58	Mutation(s): 1 Gene Names: Atu5458 EC: 5.1.2
UniProt
Find proteins for Q7D1T6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D1T6 Go to UniProtKB: Q7D1T6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7D1T6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN Query on SNN	A	L-PEPTIDE LINKING	C₄ H₆ N₂ O₂		ASN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.172 (Depositor), 0.173 (DCC)
R-Value Work: 0.153 (Depositor), 0.153 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.54	α = 90
b = 114.54	β = 90
c = 129.06	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: 2012-04-18

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-04-18
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-11-27
Changes: Structure summary