[English] 日本語
Yorodumi
- PDB-2vic: CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX with Left... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vic
TitleCRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX with Left end 26- mer DNA and manganese
Components
  • 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3'
  • TRANSPOSASE ORFA
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / PROTEIN-DNA COMPLEX / HUH MOTIF / DNA STEM LOOP / TRANSPOSITION
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA binding / metal ion binding
Similarity search - Function
Transposase IS200 like / Transposase IS200-like / Transposase IS200-like / Transposase IS200-like superfamily / Transposase IS200 like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Transposase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBarabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection.
Authors: Barabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F.
History
DepositionNov 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSPOSASE ORFA
B: TRANSPOSASE ORFA
C: 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3'
D: 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9016
Polymers52,7914
Non-polymers1102
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-25.2 kcal/mol
Surface area22170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.206, 50.261, 115.625
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.965438, -0.248876, 0.077398), (-0.254616, 0.837162, -0.484078), (0.055681, -0.487054, -0.871595)117.064, 35.699, 74.266
2given(-0.962494, -0.261095, 0.073712), (-0.26425, 0.840675, -0.472692), (0.06145, -0.474442, -0.878139)117.629, 35.336, 73.476

-
Components

#1: Protein TRANSPOSASE ORFA / TRANSPOSASE / IS608 TRANSPOSASE


Mass: 18392.430 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: PECAN2A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q933Z0
#2: DNA chain 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3' / LEFT END 26-MER


Mass: 8003.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HELICOBACTER PYLORI (bacteria)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ADDITION OF THE FIRST 5 RESIDUES (GSAMA) TO THE DATABASE SEQUENCE ARE THE RESULT OF CLONING ARTIFACT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 41.5 % / Description: SOLVED BY DIFFERENCE FOURIER METHOD
Crystal growpH: 7.5 / Details: 0.2 M SODIUM FORMATE, 15-20% PEG 3350, pH 7.5

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MULTILAYER FOCUSING MIRROR
RadiationMonochromator: MULTILAYER FOCUSING MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17657 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.5 / % possible all: 86.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VIH

2vih


Resolution: 2.35→19.47 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 598577.63 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CHAIN A CONTAINS A FLEXIBLE LOOP REGION A133-A141, THAT FEATURES WEAK ELECTRON DENSITIES AND HIGH B-FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 754 4.9 %RANDOM
Rwork0.203 ---
obs0.203 15419 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.2895 Å2 / ksol: 0.311002 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1-17.55 Å20 Å2-7.39 Å2
2---0.53 Å20 Å2
3----17.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 1041 2 111 3427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.962
X-RAY DIFFRACTIONc_scbond_it9.742
X-RAY DIFFRACTIONc_scangle_it9.722.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.471 107 4.5 %
Rwork0.367 2262 -
obs--82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARAM19.SOLMO4_XPLOR_TOP.TXT
X-RAY DIFFRACTION5MO4_XPLOR_PAR.TXTWATER.TOP

+
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