6Y1C | pdb_00006y1c

X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant D54F

PDB DOI: https://doi.org/10.2210/pdb6Y1C/pdb

Classification: OXIDOREDUCTASE
Organism(s): Levilactobacillus brevis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-02-11 Released: 2020-02-19
Deposition Author(s): Hermann, J., Bischoff, D., Janowski, R., Niessing, D., Grob, P., Hekmat, D., Weuster-Botz, D.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free:
0.162 (Depositor), 0.167 (DCC)
R-Value Work:
0.126 (Depositor), 0.131 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts

Hermann, J., Bischoff, D., Grob, P., Janowski, R., Hekmat, D., Niessing, D., Zacharias, M., Weuster-Botz, D.

(2021) Crystals (Basel) 11

DOI: https://doi.org/10.3390/cryst11060588

Macromolecule Content

Total Structure Weight: 57.08 kDa
Atom Count: 4,723
Modeled Residue Count: 502
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
R-specific alcohol dehydrogenase	A, B	262	Levilactobacillus brevis	Mutation(s): 1 Gene Names: radh
UniProt
Find proteins for Q84EX5 (Levilactobacillus brevis) Explore Q84EX5 Go to UniProtKB: Q84EX5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84EX5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B], J [auth B], K [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] L [auth B] M [auth B] O [auth B] E [auth A], F [auth A], L [auth B], M [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.162 (Depositor), 0.167 (DCC)
R-Value Work: 0.126 (Depositor), 0.131 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.76	α = 90
b = 81.09	β = 90
c = 113.13	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	WE2715/14-1

Revision History (Full details and data files)

Version 1.0: 2020-02-19
Type: Initial release
Version 1.1: 2020-03-04
Changes: Derived calculations
Version 2.0: 2020-09-23
Type: Coordinate replacement
Reason: Atomic clashes
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-06-09
Changes: Database references
Version 2.2: 2024-01-24
Changes: Data collection, Database references, Refinement description