4DHG | pdb_00004dhg

Crystal structure of enolase TBIS_1083(TARGET EFI-502310) from Thermobispora bispora dsm 43833, an open loop conformation

PDB DOI: https://doi.org/10.2210/pdb4DHG/pdb

Classification: ISOMERASE
Organism(s): Thermobispora bispora DSM 43833
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-27 Released: 2012-02-15
Deposition Author(s): Patskovsky, Y., 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:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.161 (Depositor), 0.163 (DCC)
R-Value Observed:
0.162 (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 Enolase Tbis_1083 from Thermobispora Bispora Dsm 43833

Patskovsky, Y., 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: 193.59 kDa
Atom Count: 14,103
Modeled Residue Count: 1,699
Deposited Residue Count: 1,764
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 protein	A, B, C, D	441	Thermobispora bispora DSM 43833	Mutation(s): 0 Gene Names: Tbis_1083 EC: 4.2.1.40
UniProt
Find proteins for D6Y7Y6 (Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / KCTC 9307 / NBRC 14880 / R51)) Explore D6Y7Y6 Go to UniProtKB: D6Y7Y6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D6Y7Y6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	F [auth A] H [auth A] J [auth B] M [auth B] Q [auth D] F [auth A], H [auth A], J [auth B], M [auth B], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth D], V [auth D], W [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D]	E [auth A], I [auth B], N [auth C], P [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain P [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C]	G [auth A], L [auth B], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C]
UNL Query on UNL Download:Ideal Coordinates CCD File	K [auth B]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.161 (Depositor), 0.163 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.028	α = 89.26
b = 84.823	β = 84.07
c = 94.119	γ = 72.72

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description