2EKB | pdb_00002ekb

Structural study of Project ID TTHB049 from Thermus thermophilus HB8 (L19M)

PDB DOI: https://doi.org/10.2210/pdb2EKB/pdb

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

Deposited: 2007-03-22 Released: 2007-09-25
Deposition Author(s): Asada, Y., Taketa, M., Tanaka, Y., Matsuura, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.230 (Depositor), 0.221 (DCC)
R-Value Work:
0.207 (Depositor), 0.203 (DCC)
R-Value Observed:
0.208 (Depositor)

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This is version 1.3 of the entry. See complete history.

Literature

Structural study of Project ID TTHB049 from Thermus thermophilus HB8 (L19M)

Asada, Y., Taketa, M., Tanaka, Y., Matsuura, Y., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 39.32 kDa
Atom Count: 3,158
Modeled Residue Count: 341
Deposited Residue Count: 354
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ribazole-5'-phosphate phosphatase	A, B	177	Thermus thermophilus HB8	Mutation(s): 1
UniProt
Find proteins for Q53WB3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53WB3 Go to UniProtKB: Q53WB3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53WB3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.230 (Depositor), 0.221 (DCC)
R-Value Work: 0.207 (Depositor), 0.203 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.138	α = 90
b = 91.699	β = 90
c = 110.87	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2024-05-29
Changes: Data collection

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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.