3UM9 | pdb_00003um9

Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase Bpro0530

PDB DOI: https://doi.org/10.2210/pdb3UM9/pdb

Classification: HYDROLASE
Organism(s): Polaromonas sp. JS666
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-12 Released: 2012-11-14
Deposition Author(s): Chan, P.W.Y., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.199 (Depositor), 0.195 (DCC)
R-Value Work:
0.144 (Depositor), 0.147 (DCC)
R-Value Observed:
0.147 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3UM9

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

Literature

Structural adaptations of L-2-haloacid dehalogenases that enable hydrolytic defluorination

Chan, P.W.Y., To, T.K.W., Petit, P., Tran, C., Waelti, M., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 51.37 kDa
Atom Count: 3,659
Modeled Residue Count: 450
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase, type II	A, B	230	Polaromonas sp. JS666	Mutation(s): 0 Gene Names: Bpro0530, Bpro_0530 EC: 3.8.1.2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.199 (Depositor), 0.195 (DCC)
R-Value Work: 0.144 (Depositor), 0.147 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.64	α = 90
b = 96.64	β = 90
c = 92.03	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-14
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.