[English] 日本語
Yorodumi
- PDB-2og0: Crystal Structure of the Lambda Xis-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2og0
TitleCrystal Structure of the Lambda Xis-DNA complex
Components
  • 5'-D(*AP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*AP*TP*AP*C)-3'
  • 5'-D(*GP*TP*AP*TP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*T)-3'
  • Excisionase
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DNA ARCHITECTURAL PROTEIN / 'WINGED'HELIX PROTEIN / PHAGE EXCISION / SITE-SPECIFIC RECOMBINATION 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPapagiannis, C.V. / Sam, M.D. / Abbani, M.A. / Cascio, D. / Yoo, D. / Clubb, R.T. / Johnson, R.C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Fis targets assembly of the xis nucleoprotein filament to promote excisive recombination by phage lambda.
Authors: Papagiannis, C.V. / Sam, M.D. / Abbani, M.A. / Yoo, D. / Cascio, D. / Clubb, R.T. / Johnson, R.C.
History
DepositionJan 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*GP*TP*AP*TP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*T)-3'
D: 5'-D(*AP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*AP*TP*AP*C)-3'
A: Excisionase
B: Excisionase


Theoretical massNumber of molelcules
Total (without water)23,8794
Polymers23,8794
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.483, 57.483, 163.613
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: DNA chain 5'-D(*GP*TP*AP*TP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*T)-3'


Mass: 5542.596 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*AP*TP*AP*C)-3'


Mass: 5485.622 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Excisionase


Mass: 6425.388 Da / Num. of mol.: 2 / Fragment: XIS (Residues: 1-55) / Mutation: C28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Strain: VIRUS / Gene: xis / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03699
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% Polyethylene Glycol monomethyl ether 2000, 0.2 M Ammonium Sulfate and 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1Polyethylene Glycol monomethyl ether11
2Ammonium Sulfate11
3Sodium Acetate11
4H2O11
5Polyethylene Glycol monomethyl ether12
6Ammonium Sulfate12
7Sodium Acetate12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 29, 2004 / Details: Mirrors
RadiationMonochromator: Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→80 Å / Num. all: 15654 / Num. obs: 15654 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.32 % / Biso Wilson estimate: 37.5 Å2 / Rsym value: 0.071 / Χ2: 1.038 / Net I/σ(I): 20.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.71 / Num. unique all: 1330 / Rsym value: 0.409 / Χ2: 0.996 / % possible all: 82.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RH6

1rh6


Resolution: 1.9→54.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.058 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 779 5 %RANDOM
Rwork0.191 ---
obs0.194 15573 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.393 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20.66 Å20 Å2
2--1.33 Å20 Å2
3----1.99 Å2
Refine analyzeLuzzati coordinate error free: 0.1868 Å
Refinement stepCycle: LAST / Resolution: 1.9→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 732 0 174 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211742
X-RAY DIFFRACTIONr_bond_other_d0.0020.021029
X-RAY DIFFRACTIONr_angle_refined_deg2.172.4782507
X-RAY DIFFRACTIONr_angle_other_deg1.22932491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68220.38552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8331518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
X-RAY DIFFRACTIONr_nbd_refined0.1830.2249
X-RAY DIFFRACTIONr_nbd_other0.2190.21097
X-RAY DIFFRACTIONr_nbtor_refined0.2120.2679
X-RAY DIFFRACTIONr_nbtor_other0.0860.2674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2152
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.219
X-RAY DIFFRACTIONr_mcbond_it1.21.5665
X-RAY DIFFRACTIONr_mcbond_other0.2871.5198
X-RAY DIFFRACTIONr_mcangle_it1.4332848
X-RAY DIFFRACTIONr_scbond_it2.34231623
X-RAY DIFFRACTIONr_scangle_it3.1134.51659
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 53 -
Rwork0.385 909 -
obs-962 81.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.7978-3.0741-2.87037.17432.88036.5108-0.13140.1820.1884-0.65180.2829-0.2895-0.42420.2165-0.1516-0.1284-0.0460.014-0.1392-0.0114-0.202129.58331.62842.477
23.7392-0.20190.75542.61740.17532.1326-0.0902-0.06420.15390.05860.0319-0.07090.04810.15380.0583-0.0703-0.0012-0.0311-0.1306-0.0042-0.066129.79736.12112.246
30.91420.3745-0.09241.3366-1.67862.28450.0386-0.05420.03350.03660.08230.0064-0.1663-0.2335-0.12090.04510.00390.01010.0052-0.0354-0.028316.41129.00911.754
41.2280.1118-1.32121.1807-1.22082.4562-0.08830.01250.04580.05440.13610.12610.1202-0.0625-0.0478-0.0211-0.01350.012-0.0563-0.0387-0.059117.37627.86412.236
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AC1 - 511 - 51
22BD1 - 521 - 52
33CA1 - 181 - 18
44DB19 - 361 - 18

+
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