4JD7

Crystal structure of pput_1285, a putative hydroxyproline epimerase from Pseudomonas putida f1 (target EFI-506500), open form, space group P212121, bound sulfate

PDB DOI: https://doi.org/10.2210/pdb4JD7/pdb

Classification: ISOMERASE
Organism(s): Pseudomonas putida F1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-02-24 Released: 2013-03-06
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: 1.50 Å
R-Value Free: 0.175
R-Value Work: 0.159
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of pput_1285, a putative hydroxyproline epimerase from Pseudomonas putida f1 (target EFI-506500), open form, space group P212121, bound sulfate

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.

To be published.

Macromolecule Content

Total Structure Weight: 73.69 kDa
Atom Count: 5,693
Modelled Residue Count: 626
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline racemase	A, B [auth D]	330	Pseudomonas putida F1	Mutation(s): 0 Gene Names: Pput_1285
UniProt
Find proteins for A5VZY6 (Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)) Explore A5VZY6 Go to UniProtKB: A5VZY6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5VZY6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth D], K [auth D], L [auth D], M [auth D], N [auth D], O [auth D], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175
R-Value Work: 0.159
R-Value Observed: 0.160
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.844	α = 90
b = 96.804	β = 90
c = 109.214	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: 2013-03-06

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description