[English] 日本語
Yorodumi
- PDB-6p0u: Crystal structure of ternary DNA complex " FX(1-2)-2Xis" containi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p0u
TitleCrystal structure of ternary DNA complex " FX(1-2)-2Xis" containing E. coli Fis and phage lambda Xis
Components
  • (DNA (27-MER), FX1-2) x 2
  • DNA-binding protein Fis
  • Excisionase
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA ternary complex / DNA shape / cooperative binding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / protein-DNA complex ...invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / protein-DNA complex / response to radiation / nucleosome / DNA recombination / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / cytosol
Similarity search - Function
Excisionase (Xis) protein / Excisionase-like / Excisionase-like superfamily / Excisionase-like protein / : / DNA-binding protein Fis / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Putative DNA-binding domain superfamily ...Excisionase (Xis) protein / Excisionase-like / Excisionase-like superfamily / Excisionase-like protein / : / DNA-binding protein Fis / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Putative DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Excisionase / DNA-binding protein Fis
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsHancock, S.P. / Cascio, D. / Johnson, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM038509 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Cooperative DNA binding by proteins through DNA shape complementarity.
Authors: Hancock, S.P. / Cascio, D. / Johnson, R.C.
History
DepositionMay 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding protein Fis
B: DNA-binding protein Fis
C: DNA (27-MER), FX1-2
D: DNA (27-MER), FX1-2
E: Excisionase
F: Excisionase


Theoretical massNumber of molelcules
Total (without water)52,6806
Polymers52,6806
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-74 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.850, 151.850, 120.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein DNA-binding protein Fis / Factor-for-inversion stimulation protein / Hin recombinational enhancer-binding protein


Mass: 11252.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fis, b3261, JW3229 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6R3
#2: DNA chain DNA (27-MER), FX1-2


Mass: 8295.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (27-MER), FX1-2


Mass: 8291.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Protein Excisionase


Mass: 6793.799 Da / Num. of mol.: 2 / Fragment: residues 1-55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: xis / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03699

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 7.13 Å3/Da / Density % sol: 81.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→75.92 Å / Num. obs: 20814 / % possible obs: 96 % / Redundancy: 8.139 % / Biso Wilson estimate: 76.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.114 / Χ2: 1.048 / Net I/σ(I): 15.14 / Num. measured all: 169400 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.398.3140.8192.2412396155114910.8710.87296.1
3.39-3.488.5020.7062.7312626152814850.9070.75297.2
3.48-3.588.4770.63.2912411150614640.9260.63997.2
3.58-3.698.4670.5133.8511862144514010.9520.54697
3.69-3.818.4410.3745.5211505140813630.9720.39996.8
3.81-3.958.3760.3366.1511040136613180.9730.35896.5
3.95-4.098.2990.2597.7810548131812710.9820.27696.4
4.09-4.268.0790.16311.599832126312170.9940.17496.4
4.26-4.457.9850.14413.029470123211860.9950.15496.3
4.45-4.677.3780.13114.218403117811390.9940.1496.7
4.67-4.927.0910.11914.977559111310660.9950.12995.8
4.92-5.228.5650.10717.548796107410270.9980.11495.6
5.22-5.588.4010.08321.9579819849500.9980.08896.5
5.58-6.038.3390.07624.0775729529080.9990.08195.4
6.03-6.68.2190.07525.8167238648180.9970.0894.7
6.6-7.388.1390.05234.0861047927500.9990.05594.7
7.38-8.527.6220.03943.2650767136660.9990.04293.4
8.52-10.446.6550.0348.1737205965590.9990.03293.8
10.44-14.768.1620.02563.98377149646210.02793.1
14.76-75.927.3440.02364.4520052982730.9990.02691.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.35 Å80.17 Å
Translation8.35 Å80.17 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.6.1phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IV5

3iv5


Resolution: 3.3→75.92 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU R Cruickshank DPI: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.407 / SU Rfree Blow DPI: 0.284 / SU Rfree Cruickshank DPI: 0.282
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1009 4.85 %RANDOM
Rwork0.192 ---
obs0.194 20813 96 %-
Displacement parametersBiso max: 237.25 Å2 / Biso mean: 134.17 Å2 / Biso min: 84.12 Å2
Baniso -1Baniso -2Baniso -3
1-34.4231 Å20 Å20 Å2
2--34.4231 Å20 Å2
3----68.8463 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: final / Resolution: 3.3→75.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 1101 0 0 3148
Num. residues----326
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d966SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes403HARMONIC5
X-RAY DIFFRACTIONt_it3313HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion442SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3605SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3313HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4725HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion22.33
LS refinement shellResolution: 3.3→3.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.4001 22 5.28 %
Rwork0.3017 395 -
all0.3062 417 -
obs--92.46 %
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)
19.03214.7434-0.45355.72392.32553.6770.0493-1.08851.08850.57640.22-0.3923-0.50270.0542-0.2692-0.40380.1637-0.19310.1178-0.3040.1493-3.4655-29.67824.5797
25.8291-1.4694-0.25893.9363-0.70721.5773-0.0472-0.36831.08850.3577-0.206-0.2518-0.6835-0.04240.2532-0.4210.0116-0.22-0.0508-0.30370.57592.155-24.790318.4989
36.4244-1.41782.41590.47890.44530-0.2970.1114-0.0309-0.19170.19520.13980.16760.23970.1018-0.26540.0474-0.1127-0.01990.0386-0.11491.6981-43.620811.4343
45.4416-0.74362.6640.41470.47520-0.23430.3545-0.2098-0.34660.102-0.07740.04480.28480.1323-0.34940.0834-0.0399-0.06820.09040.03051.4375-43.288210.7796
511.1507-2.02730.01987.97240.72786.32370.162-0.4049-0.5287-0.1670.05710.27870.60330.4088-0.2191-0.1423-0.0251-0.1678-0.06050.1830.1247-23.7833-46.90265.8774
60.95.8208-1.223714.5042-0.48511.96680.0910.6507-0.0104-0.5565-0.02440.35490.7998-0.2-0.0666-0.2683-0.0298-0.01170.11840.17670.025931.264-43.20514.7214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A8 - 98
2X-RAY DIFFRACTION2{ B|* }B9 - 98
3X-RAY DIFFRACTION3{ C|* }C1 - 27
4X-RAY DIFFRACTION4{ D|* }D1 - 27
5X-RAY DIFFRACTION5{ E|* }E1 - 52
6X-RAY DIFFRACTION6{ F|* }F1 - 51

+
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