8QPS | pdb_00008qps

Deoxyribose-5-phosphate aldolase (DERA) from Geobacillus sp.

PDB DOI: https://doi.org/10.2210/pdb8QPS/pdb

Classification: LYASE
Organism(s): Geobacillus sp.
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-03 Released: 2024-10-16
Deposition Author(s): Paakkonen, J., Hakulinen, N., Rouvinen, J.
Funding Organization(s): Academy of Finland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Three-dimensional structure of deoxyribose phosphate aldolase (DERA) from thermophilic Geobacillus sp.

Paakkonen, J., Andberg, M., Voutilainen, S., Koivula, A., Hakulinen, N., Janis, J., Rouvinen, J.

To be published.

Macromolecule Content

Total Structure Weight: 48.53 kDa
Atom Count: 3,578
Modeled Residue Count: 440
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribose-phosphate aldolase	A, B	230	Geobacillus sp.	Mutation(s): 0 Gene Names: deoC EC: 4.1.2.4
UniProt
Find proteins for Q5KX02 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KX02 Go to UniProtKB: Q5KX02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5KX02
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.192 (Depositor), 0.192 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.23	α = 90
b = 57.23	β = 90
c = 97.03	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
xia2	data reduction
DIALS	data reduction
XDS	data reduction
XSCALE	data scaling
Aimless	data scaling
pointless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Academy of Finland	Finland	288677
Academy of Finland	Finland	287241
Academy of Finland	Finland	321514
Academy of Finland	Finland	321503

Revision History (Full details and data files)

Version 1.0: 2024-10-16
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.