[English] 日本語
Yorodumi
- PDB-1jj8: Testing the Water-Mediated HIN Recombinase DNA Recognition by Sys... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jj8
TitleTesting the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations
Components
  • 5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'
  • 5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'
  • DNA-INVERTASE HIN
KeywordsDNA BINDING PROTEIN/DNA / WATER-MEDIATED RECOGNITION / PROTEIN-DNA COMPLEX / HIN RECOMBINASE / I4 FORM 2 / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA recombination / DNA binding
Similarity search - Function
Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain ...Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-invertase hin
Similarity search - Component
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.75 Å
AuthorsChiu, T.K. / Sohn, C. / Johnson, R.C. / Dickerson, R.E.
Citation
Journal: EMBO J. / Year: 2002
Title: Testing water-mediated DNA recognition by the Hin recombinase.
Authors: Chiu, T.K. / Sohn, C. / Dickerson, R.E. / Johnson, R.C.
#1: Journal: Thesis / Year: 2001
Title: How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase.
Authors: Chiu, T.K.
#2: Journal: Science / Year: 1994
Title: Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions.
Authors: Feng, J.A. / Johnson, R.C. / Dickerson, R.E.
History
DepositionJul 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 4, 2015Group: Database references / Other
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'
B: 5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'
C: DNA-INVERTASE HIN


Theoretical massNumber of molelcules
Total (without water)14,7163
Polymers14,7163
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.328, 68.693, 62.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-212-

HOH

-
Components

#1: DNA chain 5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'


Mass: 4436.707 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'


Mass: 4231.806 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA-INVERTASE HIN / Hin Recombinase


Mass: 6047.051 Da / Num. of mol.: 1 / Fragment: RESIDUES 139 TO 190 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / References: UniProt: P03013
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.423 Å3/Da / Density % sol: 47.27 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: 0.08 MM DNA, 0.04 MM HIN, 25 MM NA ACETATE (PH 4.6), 25 MM MGCL2, 8 MM NACL, 6.3% V/V PEG400, AND 1.25 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM NA ACETATE (PH 4.6), 100 MM MGCL2, ...Details: 0.08 MM DNA, 0.04 MM HIN, 25 MM NA ACETATE (PH 4.6), 25 MM MGCL2, 8 MM NACL, 6.3% V/V PEG400, AND 1.25 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM NA ACETATE (PH 4.6), 100 MM MGCL2, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%. CONDITIONS FOR NATIVE ARE THE SAME EXCEPT THE CONCENTRATION OF MGCL2 IS 5 TIMES SMALLER., pH 4.60, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1DNA11
2HIN11
3sodium acetate11
4MgCl211
5NaCl11
6PEG 40011
7sodium cacodylate11
8sodium acetate12
9MgCl212
10PEG 40012
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 4.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120-100 mM1reservoirMgCl2
2100 mM1reservoirNaOAcpH4.6
325 %PEG4001reservoir
41
51
61
71
81
91
101

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.543
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.543 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 3765 / % possible obs: 96.49 % / Observed criterion σ(I): 1 / Redundancy: 15 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.081 / Net I/σ(I): 19.6
Reflection shellResolution: 2.75→2.87 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.267 / % possible all: 91.64
Reflection
*PLUS
% possible obs: 96.5 % / Redundancy: 15 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 91.6 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.9

-
Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: SIRAS PHASES

Resolution: 2.75→25 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: ANISOTROPIC_FIXED_ISOTROPIC / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 369 9.46 %RANDOM
Rwork0.2134 ---
obs0.2134 3765 96.49 %-
Solvent computationBsol: 18.88 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-9.45 Å20 Å20 Å2
2---5.107 Å20 Å2
3----4.343 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms375 552 0 12 939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.41
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.45
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.632.05
LS refinement shellResolution: 2.75→2.87 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.5136 45 9.39 %
Rwork0.3529 394 -
obs--91.64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.41
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.45
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scangle_it3.632.05
LS refinement shell
*PLUS
Rfactor obs: 0.353

+
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