[English] 日本語
Yorodumi
- PDB-1rh6: Bacteriophage Lambda Excisionase (Xis)-DNA Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rh6
TitleBacteriophage Lambda Excisionase (Xis)-DNA Complex
Components
  • 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'
  • 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'
  • Excisionase
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / DNA architectural protein / 'winged'-helix protein / phage excision / site-specific DNA recombination / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


provirus excision / DNA recombination / DNA binding / identical protein binding
Similarity search - Function
Excisionase (Xis) protein / Excisionase-like / Excisionase-like superfamily / Excisionase-like protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Excisionase
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsSam, M.D. / Cascio, D. / Johnson, R.C. / Clubb, R.T.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the excisionase-DNA complex from bacteriophage lambda.
Authors: Sam, M.D. / Cascio, D. / Johnson, R.C. / Clubb, R.T.
History
DepositionNov 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Derived calculations
Revision 1.4Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_validate_close_contact / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'
D: 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'
A: Excisionase
B: Excisionase


Theoretical massNumber of molelcules
Total (without water)22,7654
Polymers22,7654
Non-polymers00
Water2,738152
1
C: 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'
D: 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'
B: Excisionase


Theoretical massNumber of molelcules
Total (without water)15,9713
Polymers15,9713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Excisionase


Theoretical massNumber of molelcules
Total (without water)6,7941
Polymers6,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.215, 72.691, 38.801
Angle α, β, γ (deg.)90.00, 104.11, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: DNA chain 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'


Mass: 4605.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'


Mass: 4571.015 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Excisionase


Mass: 6793.799 Da / Num. of mol.: 2 / Fragment: Xis DBD (residues 1-55) / Mutation: C28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: xis / Plasmid: pet11a / Production host: Escherichia coli (E. coli) / Strain (production host): RJ3386 (BL21-DE3) / References: UniProt: P03699
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NaOAc, imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaOAc11
2imidazole11
3H2O11
4NaOAc12
5imidazole12
6H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 32190 / % possible obs: 93.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 93.1 % / Biso Wilson estimate: 24.125 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 19.8
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 95.8 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 8.2 / Num. unique all: 3280 / Rsym value: 0.152 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.618 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22553 1161 5 %RANDOM
Rwork0.19117 ---
all0.19293 ---
obs0.19293 21990 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.551 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å21.19 Å2
2---1.23 Å20 Å2
3----1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.108 Å0.11 Å
Luzzati d res low-20 Å
Luzzati sigma a-0.086 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 574 0 152 1657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211598
X-RAY DIFFRACTIONr_bond_other_d0.0020.021173
X-RAY DIFFRACTIONr_angle_refined_deg2.5822.3972278
X-RAY DIFFRACTIONr_angle_other_deg1.20232752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021329
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02241
X-RAY DIFFRACTIONr_nbd_refined0.2230.2239
X-RAY DIFFRACTIONr_nbd_other0.250.21286
X-RAY DIFFRACTIONr_nbtor_other0.0920.2773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.420.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4711.5539
X-RAY DIFFRACTIONr_mcangle_it2.4642882
X-RAY DIFFRACTIONr_scbond_it3.10231059
X-RAY DIFFRACTIONr_scangle_it4.4924.51396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 78
Rwork0.23 1613

+
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://pdbjlc1.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