4E4F | pdb_00004e4f

Crystal structure of enolase PC1_0802 (TARGET EFI-502240) from Pectobacterium carotovorum subsp. carotovorum PC1

PDB DOI: https://doi.org/10.2210/pdb4E4F/pdb

Classification: ISOMERASE
Organism(s): Pectobacterium carotovorum subsp. carotovorum PC1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-12 Released: 2012-03-28
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:
0.245 (Depositor), 0.245 (DCC)
R-Value Work:
0.188 (Depositor), 0.192 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of ENOLASE PC1_0802 from Pectobacterium carotovorum

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: 194.28 kDa
Atom Count: 13,154
Modeled Residue Count: 1,536
Deposited Residue Count: 1,704
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNONATE DEHYDRATASE	A, B, C, D	426	Pectobacterium carotovorum subsp. carotovorum PC1	Mutation(s): 0 Gene Names: PC1_0802 EC: 4.2.1 (UniProt), 4.2.1.8 (UniProt)
UniProt
Find proteins for C6D9S0 (Pectobacterium carotovorum subsp. carotovorum (strain PC1)) Explore C6D9S0 Go to UniProtKB: C6D9S0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6D9S0
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 K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth D]	E [auth A] G [auth A] I [auth A] K [auth B] L [auth B] E [auth A], G [auth A], I [auth A], K [auth B], L [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], V [auth D], W [auth D], Y [auth D]	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 K [auth B] Focus chain L [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	J [auth A], P [auth B], U [auth C], Z [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain J [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	H [auth A], O [auth B], T [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.245 (Depositor), 0.245 (DCC)
R-Value Work: 0.188 (Depositor), 0.192 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.278	α = 90
b = 86.338	β = 123.07
c = 114.463	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-28

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-03-28
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description