4J9W

Crystal structure of the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with the inhibitor pyrrole-2-carboxylate

PDB DOI: https://doi.org/10.2210/pdb4J9W/pdb

Classification: Isomerase/Isomerase Inhibitor complex
Organism(s): Pseudomonas protegens Pf-5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-02-17 Released: 2013-03-13
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.232
R-Value Work: 0.197
R-Value Observed: 0.199

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 the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with the inhibitor pyrrole-2-carboxylate

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 72.62 kDa
Atom Count: 5,301
Modelled Residue Count: 620
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline racemase family protein	A, B	332	Pseudomonas protegens Pf-5	Mutation(s): 0 Gene Names: PFL_1412 EC: 5.1.1.8
UniProt
Find proteins for Q4KGU2 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KGU2 Go to UniProtKB: Q4KGU2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4KGU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PYC Query on PYC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	PYRROLE-2-CARBOXYLATE C₅ H₄ N O₂ WRHZVMBBRYBTKZ-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B]	C [auth A], F [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.232
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.174	α = 90
b = 74.637	β = 105.46
c = 87.048	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-13

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-03-13
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description