[English] 日本語
Yorodumi
- PDB-1j6o: Crystal structure of TatD-related deoxyribonuclease (TM0667) from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j6o
TitleCrystal structure of TatD-related deoxyribonuclease (TM0667) from Thermotoga maritima at 1.8 A resolution
ComponentsTatD-related deoxyribonuclease
KeywordsHYDROLASE / structural genomics / TM0667 / TatD-related deoxyribonuclease / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


DNA nuclease activity / metal ion binding / cytosol
Similarity search - Function
Uncharacterised hydrolase TatD-type / 3'-5' ssDNA/RNA exonuclease TatD-like / TatD related DNase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of TatD-related deoxyribonuclease (TM0667) from Thermotoga maritima at 1.8 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Advisory / Data collection / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN The "putative" binuclear metal is most likely conserved in TM0667, but no metals were ...HETEROGEN The "putative" binuclear metal is most likely conserved in TM0667, but no metals were found in the structure. One of the metal sites is occupied by a water molecule.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TatD-related deoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8382
Polymers30,7781
Non-polymers601
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.05, 77.25, 84.53
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TatD-related deoxyribonuclease


Mass: 30777.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0667 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZD5, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.36 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 19 % iso-Propanol/19 % PEG 4000; 0.095 M citrate pH 5.6, 5 % Glycerol, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 5.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.918370, 0.979224, 0.978932
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2002
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9792241
30.9789321
ReflectionResolution: 1.8→29.86 Å / Num. obs: 21717 / % possible obs: 98.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 11.2 Å2 / Rsym value: 0.104 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.539 / % possible all: 87.1

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
SnBphasing
MLPHAREphasing
CCP4model building
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.88 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
Details: CIS-PEPTIDE AT POSITION GLY89. ONE VERY INTERESTING FEATURE OF PHOSPHOTRIESTERASE IS THAT A CARBAMYLATED LYSINE RESIDUE (LYS 169) IS NEEDED FOR CATALYST, THIS ENDS UP LOOKING LIKE AN ...Details: CIS-PEPTIDE AT POSITION GLY89. ONE VERY INTERESTING FEATURE OF PHOSPHOTRIESTERASE IS THAT A CARBAMYLATED LYSINE RESIDUE (LYS 169) IS NEEDED FOR CATALYST, THIS ENDS UP LOOKING LIKE AN EXTENDED GLU. IN TM0667 THIS POSITION OF THE CARBOXY GROUP FROM THE CARBAMYLATED LYSINE IS REPLACED BY A GLU90. IN ORDER TO REACH THE ACTIVE SITE GLU90 HAS TO REACH OUT, CAUSING A BULGE IN THE BETA SHEET. GLU90 IS PRECEDED BY A GLY WITH ADOPTS A CIS CONFIRMATION TO ACCOMMODATED THE BULGE.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1051 4.9 %RANDOM
Rwork0.19 ---
obs0.19 21648 98.5 %-
all-21648 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 36.05 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---1.84 Å20 Å2
3---1.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 0 199 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.77
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 1.8→1.83 Å / Total num. of bins used: 21
RfactorNum. reflection% reflection
Rfree0.243 44 5.1 %
Rwork0.2228 820 -

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more