5LKA | pdb_00005lka

Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+211L mutant (LinB86) from Sphingobium japonicum UT26 at 1.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb5LKA/pdb

Classification: HYDROLASE
Organism(s): Sphingobium indicum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-07-21 Released: 2016-10-05
Deposition Author(s): Degtjarik, O., Rezacova, P., Iermak, I., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.174 (Depositor), 0.176 (DCC)
R-Value Work:
0.139 (Depositor), 0.139 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5LKA

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

Literature

Engineering a de novo transport tunnel.

Brezovsky, J., Babkova, P., Degtjarik, O., Fortova, A., Gora, A., Iermak, I., Rezacova, P., Dvorak, P., Kuta Smatanova, I., Prokop, Z., Chaloupkova, R., Damborsky, J.

(2016) ACS Catal

DOI: https://doi.org/10.1021/acscatal.6b02081

Macromolecule Content

Total Structure Weight: 33.82 kDa
Atom Count: 2,988
Modeled Residue Count: 301
Deposited Residue Count: 301
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	301	Sphingobium indicum	Mutation(s): 4 Gene Names: linB, dhaA, SJA_C1-19590 EC: 3.8.1.5
UniProt
Find proteins for D4Z2G1 (Sphingobium indicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S)) Explore D4Z2G1 Go to UniProtKB: D4Z2G1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D4Z2G1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SCN Query on SCN 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]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-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: 1.30 Å
R-Value Free: 0.174 (Depositor), 0.176 (DCC)
R-Value Work: 0.139 (Depositor), 0.139 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.867	α = 90
b = 68.362	β = 90
c = 80.648	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Chaloupkova, R.

Kuta Smatanova, I.

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.