3TOY

CRYSTAL STRUCTURE OF ENOLASE BRADO_4202 (TARGET EFI-501651) FROM Bradyrhizobium sp. ORS278 WITH CALCIUM AND ACETATE BOUND

PDB DOI: https://doi.org/10.2210/pdb3TOY/pdb

Classification: LYASE
Organism(s): Bradyrhizobium sp. ORS 278
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-09-06 Released: 2011-09-21
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., Hammond, 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: 0.199
R-Value Work: 0.158
R-Value Observed: 0.160

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF MANDELATE RACEMASE FROM Bradyrhizobium sp. ORS278

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

To be published.

Macromolecule Content

Total Structure Weight: 167.34 kDa
Atom Count: 12,537
Modelled Residue Count: 1,436
Deposited Residue Count: 1,532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme family protein	A, B, C, D	383	Bradyrhizobium sp. ORS 278	Mutation(s): 0 Gene Names: BRADO4202 EC: 5.1.2.2 (PDB Primary Data), 5.5.1.1 (PDB Primary Data)
UniProt
Find proteins for A4YVM8 (Bradyrhizobium sp. (strain ORS 278)) Explore A4YVM8 Go to UniProtKB: A4YVM8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4YVM8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4C Query on P4C Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	H [auth A] M [auth B] N [auth B] R [auth C] S [auth C] H [auth A], M [auth B], N [auth B], R [auth C], S [auth C], X [auth D]	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL C₁₄ H₂₈ O₈ CTLLATPOKUEFSQ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	F [auth A], K [auth B], Q [auth C], V [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain W [auth D]	G [auth A], L [auth B], W [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain W [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain I [auth A] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain I [auth A] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain I [auth A] mmCIF format, chain U [auth D]	E [auth A] I [auth A] J [auth B] O [auth B] P [auth C] E [auth A], I [auth A], J [auth B], O [auth B], P [auth C], T [auth C], U [auth D], Y [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.199
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.389	α = 90
b = 131.838	β = 90
c = 108.825	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2012-02-22
Changes: Database references, Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description