4IT1 | pdb_00004it1

Crystal structure of enolase pfl01_3283 (target efi-502286) from pseudomonas fluorescens pf0-1 with bound magnesium, potassium and tartrate

PDB DOI: https://doi.org/10.2210/pdb4IT1/pdb

Classification: ISOMERASE
Organism(s): Pseudomonas fluorescens Pf0-1
Mutation(s): No

Deposited: 2013-01-17 Released: 2013-01-30
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., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.250 (Depositor), 0.248 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (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 Pfl01_3283 from Pseudomonas Fluorescens

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., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 198.73 kDa
Atom Count: 14,027
Modeled Residue Count: 1,704
Deposited Residue Count: 1,784
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glucarate dehydratase	A, B, C, D	446	Pseudomonas fluorescens Pf0-1	Mutation(s): 0 Gene Names: Pfl01_3283 EC: 4.2.1.40
UniProt
Find proteins for Q3KB33 (Pseudomonas fluorescens (strain Pf0-1)) Explore Q3KB33 Go to UniProtKB: Q3KB33
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3KB33
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B]	F [auth A], G [auth B], I [auth C], L [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C]	H [auth B], J [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain H [auth B] Focus chain J [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain E [auth A]	E [auth A], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.250 (Depositor), 0.248 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.321	α = 90
b = 147.695	β = 90
c = 173.195	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: 2013-01-30

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-01-30
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description