[English] 日本語
Yorodumi
- PDB-3hd0: Crystal structure of Tm1865, an Endonuclease V from Thermotoga Ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hd0
TitleCrystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima
ComponentsEndonuclease V
KeywordsHYDROLASE / structural genomics / ISFI / RNaseH SUPERFAMILY / Endonuclease V / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / Cytoplasm / DNA damage / DNA repair / Endonuclease / Magnesium / Nuclease
Function / homology
Function and homology information


deoxyribonuclease V / deoxyribonuclease V activity / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / single-stranded RNA binding / DNA repair / magnesium ion binding / cytoplasm
Similarity search - Function
: / Endonuclease V / Endonuclease V / archaeoglobus fulgidus dsm 4304 fold / archaeoglobus fulgidus dsm 4304 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsUtepbergenov, D. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: To be Published
Title: Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima
Authors: Utepbergenov, D. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease V
B: Endonuclease V
D: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)81,9963
Polymers81,9963
Non-polymers00
Water3,981221
1
A: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)27,3321
Polymers27,3321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)27,3321
Polymers27,3321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)27,3321
Polymers27,3321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.571, 71.966, 120.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer.

-
Components

#1: Protein Endonuclease V / Deoxyinosine 3'endonuclease / Deoxyribonuclease V / DNase V


Mass: 27332.053 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nfi, TM_1865 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9X2H9, deoxyribonuclease V
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.84 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris pH 8.5, 100 mM NaCl and 24 w/v% PEG 1500, 20% glycerol. The crystallization reservoir was 1.5 M NaCl, VAPOR DIFFUSION, ...Details: Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris pH 8.5, 100 mM NaCl and 24 w/v% PEG 1500, 20% glycerol. The crystallization reservoir was 1.5 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97876, 0.97860, 0.97243
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978761
20.97861
30.972431
ReflectionResolution: 2.7→50 Å / Num. obs: 17147 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.333
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.27 / % possible all: 99.8

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97865.1-8.04
3 wavelength120.97873.15-9.84
3 wavelength130.97113.99-3.36
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se55.9020.030.1440.810.945
2Se16.4520.0740.4680.8720.582
3Se33.670.5020.4270.8290.829
4Se39.8550.560.5860.7340.808
5Se54.4220.9780.6910.9890.848
6Se58.0520.850.340.7070.987
7Se40.4860.2060.2050.6590.689
8Se43.850.8770.1420.9140.816
9Se54.0580.7960.5720.0390.855
10Se45.9530.9390.9610.9020.649
11Se600.3390.4890.7690.674

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.597 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25518 890 5.2 %RANDOM
Rwork0.16275 ---
obs0.16742 16183 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.75 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5291 0 0 221 5512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225451
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9927352
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16922.478226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.99315972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1321544
X-RAY DIFFRACTIONr_chiral_restr0.1060.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024070
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.22665
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23681
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.2136
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4911.53361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.58325353
X-RAY DIFFRACTIONr_scbond_it4.02532325
X-RAY DIFFRACTIONr_scangle_it6.6464.51999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.703→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 76 -
Rwork0.244 1148 -
obs--99.67 %

+
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