6G75

Crystal structure of the common ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc)

PDB DOI: https://doi.org/10.2210/pdb6G75/pdb

Classification: HYDROLASE
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-04 Released: 2019-04-24
Deposition Author(s): Chaloupkova, R., Waterman, J., Marek, M., Damborsky, J.
Funding Organization(s): Grant Agency of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.190
R-Value Work: 0.150
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

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

Literature

Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts

Chaloupkova, R., Liskova, V., Toul, M., Markova, K., Sebestova, E., Hernychova, L., Marek, M., Pinto, G.P., Pluskal, D., Waterman, J., Prokop, Z., Damborsky, J.

(2019) ACS Catal

DOI: https://doi.org/10.1021/acscatal.9b01031

Macromolecule Content

Total Structure Weight: 68.63 kDa
Atom Count: 5,368
Modelled Residue Count: 592
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Common ancestor of haloalkane dehalogenase and Renilla luciferase (AncHLD-RLuc)	A, B	296	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.190
R-Value Work: 0.150
R-Value Observed: 0.152
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.549	α = 90
b = 60.51	β = 90.9
c = 123.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	16-24223S

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release
Version 1.1: 2020-05-06
Changes: Database references
Version 1.2: 2024-01-17
Changes: Advisory, Data collection, Database references, Refinement description

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Help and Resources

6G75

Crystal structure of the common ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc)

Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts

Entity ID: 1

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)