4F60

Crystal structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant (T148L, G171Q, A172V, C176F).

PDB DOI: https://doi.org/10.2210/pdb4F60/pdb

Classification: HYDROLASE
Organism(s): Rhodococcus rhodochrous
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-05-14 Released: 2013-01-23
Deposition Author(s): Plevaka, M., Kuta-Smatanova, I., Rezacova, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.171
R-Value Work: 0.150
R-Value Observed: 0.151

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel.

Koudelakova, T., Chaloupkova, R., Brezovsky, J., Prokop, Z., Sebestova, E., Hesseler, M., Khabiri, M., Plevaka, M., Kulik, D., Kuta Smatanova, I., Rezacova, P., Ettrich, R., Bornscheuer, U.T., Damborsky, J.

(2013) Angew Chem Int Ed Engl 52: 1959-1963

PubMed: 23303607 Search on PubMed
DOI: https://doi.org/10.1002/anie.201206708
Primary Citation of Related Structures:
4F5Z, 4F60

Organizational Affiliation

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

Macromolecule Content

Total Structure Weight: 34.29 kDa
Atom Count: 2,884
Modelled Residue Count: 290
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	299	Rhodococcus rhodochrous	Mutation(s): 4 Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P0A3G2 (Rhodococcus rhodochrous) Explore P0A3G2 Go to UniProtKB: P0A3G2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A3G2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F Query on F 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]	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.171
R-Value Work: 0.150
R-Value Observed: 0.151
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.018	α = 90
b = 69.93	β = 90
c = 85.352	γ = 90

Software Package:

Software Name	Purpose
MarDB	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-01-23

Deposition Author(s):

Plevaka, M.

Kuta-Smatanova, I.

Rezacova, P.

Revision History (Full details and data files)

Version 1.0: 2013-01-23
Type: Initial release
Version 1.1: 2013-02-27
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description