6S42 | pdb_00006s42

The double mutant(Ile44Leu+Gln102His) of haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94 with an eliminated halide-binding site

PDB DOI: https://doi.org/10.2210/pdb6S42/pdb

Classification: HYDROLASE
Organism(s): Bradyrhizobium elkanii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-06-26 Released: 2020-02-05
Deposition Author(s): Pudnikova, T., Mesters, J.R., Kuta Smatanova, I.
Funding Organization(s): Grant Agency of the Czech Republic, German Federal Ministry for Education and Research, European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.152 (Depositor), 0.154 (DCC)
R-Value Work:
0.140 (Depositor), 0.141 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystallization and Crystallographic Analysis of a Bradyrhizobium Elkanii USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site

Prudnikova, T., Kuta Smatanova, I.

(2019) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst9070375

Macromolecule Content

Total Structure Weight: 35.23 kDa
Atom Count: 2,822
Modeled Residue Count: 292
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	310	Bradyrhizobium elkanii	Mutation(s): 2 Gene Names: dbeA, dhaA EC: 3.8.1.5
UniProt
Find proteins for E2RV62 (Bradyrhizobium elkanii) Explore E2RV62 Go to UniProtKB: E2RV62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E2RV62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD (Subject of Investigation/LOI) Query on IOD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	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 A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		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 A] 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 A]
HEZ (Subject of Investigation/LOI) Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.152 (Depositor), 0.154 (DCC)
R-Value Work: 0.140 (Depositor), 0.141 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.945	α = 90
b = 63.95	β = 106.27
c = 46.053	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Pudnikova, T.

Mesters, J.R.

Kuta Smatanova, I.

Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	17-24321S
German Federal Ministry for Education and Research	Germany	DAAD-16-19
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/15_003/0000441
European Regional Development Fund	Czech Republic	LM2015055