1J6O | pdb_00001j6o

Crystal structure of TatD-related deoxyribonuclease (TM0667) from Thermotoga maritima at 1.8 A resolution

PDB DOI: https://doi.org/10.2210/pdb1J6O/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-07-09 Released: 2002-10-30
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.224 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1J6O

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of TatD-related deoxyribonuclease (TM0667) from Thermotoga maritima at 1.8 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 30.84 kDa
Atom Count: 2,296
Modeled Residue Count: 260
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TatD-related deoxyribonuclease	A	268	Thermotoga maritima	Mutation(s): 1 Gene Names: TM0667 EC: 3.1.21
UniProt
Find proteins for Q9WZD5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZD5 Go to UniProtKB: Q9WZD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.224 (Depositor), 0.230 (DCC)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)
R-Value Observed: 0.190 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.05	α = 90
b = 77.25	β = 90
c = 84.53	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
CCP4	data reduction
SnB	phasing
MLPHARE	phasing
CCP4	model building
SOLVE	phasing
CNS	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-10-30

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2002-10-30
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-07-18
Changes: Advisory, Data collection, Database references
Version 1.4: 2023-01-25
Changes: Advisory, Database references, Derived calculations
Version 1.5: 2024-11-13
Changes: Data collection, Structure summary

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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.