8PA1 | pdb_00008pa1

Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form

PDB DOI: https://doi.org/10.2210/pdb8PA1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-06-07 Released: 2024-06-26
Deposition Author(s): Rozeboom, H.J., Janssen, D.B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.241 (Depositor), 0.249 (DCC)
R-Value Work:
0.177 (Depositor), 0.185 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PA1

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form

Delgado-Arciniega, E., Bodescu, V., Rozeboom, H.J., Janssen, D.B., Wijma, H.J.

To be published.

Macromolecule Content

Total Structure Weight: 113.37 kDa
Atom Count: 7,660
Modeled Residue Count: 996
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, short-chain dehydrogenase/reductase family	A, B, C, D	264	Thermus thermophilus HB8	Mutation(s): 8 Gene Names: TTHA0369
UniProt
Find proteins for Q5SLC4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLC4 Go to UniProtKB: Q5SLC4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SLC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], K [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], I [auth C], L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.241 (Depositor), 0.249 (DCC)
R-Value Work: 0.177 (Depositor), 0.185 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.538	α = 90
b = 95.455	β = 108.06
c = 79.016	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-06-26
Type: Initial release

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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.