4K7X | pdb_00004k7x

Crystal structure of a 4-hydroxyproline epimerase from burkholderia multivorans, target efi-506479, with bound phosphate, closed domains

PDB DOI: https://doi.org/10.2210/pdb4K7X/pdb

Classification: LYASE
Organism(s): Burkholderia multivorans ATCC 17616
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-17 Released: 2013-05-01
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., 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: 1.75 Å
R-Value Free:
0.156 (Depositor), 0.157 (DCC)
R-Value Work:
0.137 (Depositor), 0.139 (DCC)
R-Value Observed:
0.138 (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 a 4-hydroxyproline epimerase from burkholderia multivorans, target efi-506479, with bound phosphate, closed domains

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., 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: 36.12 kDa
Atom Count: 2,904
Modeled Residue Count: 314
Deposited Residue Count: 333
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline racemase	A	333	Burkholderia multivorans ATCC 17616	Mutation(s): 0 Gene Names: prdF, BMULJ_04062 EC: 5.1.1.4 (PDB Primary Data), 5.1.1.8 (UniProt)
UniProt
Find proteins for B3D6W2 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore B3D6W2 Go to UniProtKB: B3D6W2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3D6W2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.156 (Depositor), 0.157 (DCC)
R-Value Work: 0.137 (Depositor), 0.139 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.885	α = 90
b = 114.885	β = 90
c = 173.699	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-05-01

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-05-01
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description