4FI4 | pdb_00004fi4

Crystal structure of mannonate dehydratase PRK15072 (TARGET EFI-502214) from Caulobacter sp. K31

PDB DOI: https://doi.org/10.2210/pdb4FI4/pdb

Classification: ISOMERASE
Organism(s): Caulobacter sp. K31
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-06-07 Released: 2012-06-27
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: 2.00 Å
R-Value Free:
0.204 (Depositor), 0.206 (DCC)
R-Value Work:
0.149 (Depositor), 0.152 (DCC)
R-Value Observed:
0.151 (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 Prk15072 (Target Efi-502214) from Caulobacter Sp. K31

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: 143.18 kDa
Atom Count: 10,548
Modeled Residue Count: 1,213
Deposited Residue Count: 1,275
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	425	Caulobacter sp. K31	Mutation(s): 0 Gene Names: Caul_1427 EC: 4.2.1.8
UniProt
Find proteins for B0T0B1 (Caulobacter sp. (strain K31)) Explore B0T0B1 Go to UniProtKB: B0T0B1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0T0B1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth C]	E [auth A] G [auth A] I [auth A] J [auth A] M [auth B] E [auth A], G [auth A], I [auth A], J [auth A], M [auth B], O [auth B], P [auth B], Q [auth B], S [auth C], T [auth C], U [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C]	F [auth A], H [auth A], K [auth A], N [auth B], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain V [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C]	D [auth A], L [auth B], R [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain L [auth B] Focus chain R [auth C]
UNL Query on UNL Download:Ideal Coordinates CCD File	W [auth C]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.204 (Depositor), 0.206 (DCC)
R-Value Work: 0.149 (Depositor), 0.152 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.617	α = 90
b = 137.617	β = 90
c = 264.696	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: 2012-06-27

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-06-27
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description