[English] 日本語
Yorodumi
- PDB-3jra: Crystal structure of Fis bound to 27bp non consensus sequence DNA F6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jra
TitleCrystal structure of Fis bound to 27bp non consensus sequence DNA F6
Components
  • (DNA (27-MER)) x 2
  • DNA-binding protein fis
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / HTH domain / minor groove compression / DNA bending / indirect recognition / activator / DNA-binding / Transcription / Transcription regulation / 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 / response to radiation ...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 / response to radiation / protein-DNA complex / nucleosome / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / cytosol
Similarity search - Function
DNA-binding protein Fis / : / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding protein Fis
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3IV5 / Resolution: 3.11 Å
AuthorsStella, S. / Cascio, D. / Johnson, R.C.
CitationJournal: Genes Dev. / Year: 2010
Title: The shape of the DNA minor groove directs binding by the DNA-bending protein Fis.
Authors: Stella, S. / Cascio, D. / Johnson, R.C.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)
D: DNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)39,0914
Polymers39,0914
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-62 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.240, 95.220, 154.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA-binding protein fis


Mass: 11252.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: fis, b3261, JW3229 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6R3
#2: DNA chain DNA (27-MER)


Mass: 8254.367 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8330.447 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 36% PEG 400, vapor diffusion, hanging drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→90 Å / Num. obs: 11963 / % possible obs: 97.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.139 / Χ2: 1.825 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.214.50.4539881.087184.2
3.21-3.345.20.46311385.5194.8
3.34-3.496.40.4311762.946199
3.49-3.687.20.37112082.291100
3.68-3.917.60.30712072.1811100
3.91-4.217.50.17712011.05199.9
4.21-4.637.20.11912060.9481100
4.63-5.36.80.11812401.021100
5.3-6.686.50.11412461.12199.9
6.68-908.40.05913531.307199.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: 3IV5 / Resolution: 3.11→81.11 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.384 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 9.911 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 527 4.8 %RANDOM
Rwork0.238 ---
obs0.24 10999 90.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.28 Å2 / Biso mean: 48.163 Å2 / Biso min: 15.81 Å2
Refinement stepCycle: LAST / Resolution: 3.11→81.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 8 2614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222752
X-RAY DIFFRACTIONr_bond_other_d0.0010.021523
X-RAY DIFFRACTIONr_angle_refined_deg1.3312.473942
X-RAY DIFFRACTIONr_angle_other_deg1.0333785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1125.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41415303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9891511
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0550.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
X-RAY DIFFRACTIONr_nbd_refined0.2090.2640
X-RAY DIFFRACTIONr_nbd_other0.1920.21771
X-RAY DIFFRACTIONr_nbtor_refined0.2070.21207
X-RAY DIFFRACTIONr_nbtor_other0.0820.21175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.27
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)0.281.51229
X-RAY DIFFRACTIONMAIN-CHAIN BOND OTHER ATOMS (A''2)0.031.5382
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)0.31221511
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)0.42232352
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)0.7014.52431
LS refinement shellResolution: 3.11→3.191 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 9 -
Rwork0.298 142 -
all-151 -
obs--17.6 %
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)
11.9047-1.35230.85696.2782-0.72493.8274-0.1649-0.04-0.07450.54570.1713-0.20720.48750.2801-0.0063-0.3989-0.0198-0.0022-0.1690.0078-0.342612.843711.18938.8456
23.11661.3736-0.72195.5733-0.29223.2082-0.045-0.2433-0.02750.11910.02850.19090.14810.060.0164-0.45780.0623-0.0219-0.18640.0288-0.35759.743411.67062.1159
31.59130.14392.86251.15860.970410.89060.55330.0454-0.72320.26550.26030.08762.08690.4582-0.81360.28240.0936-0.0194-0.09130.0378-0.082711.5215-9.62475.2404
41.9763-0.09863.92420.6135-0.208515.73950.4779-0.0924-0.73390.17350.2873-0.04011.8512-0.1477-0.76520.3169-0.0275-0.075-0.2194-0.0022-0.036810.6129-9.69216.0444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 98
2X-RAY DIFFRACTION2B1 - 98
3X-RAY DIFFRACTION3C1 - 27
4X-RAY DIFFRACTION4D1 - 27

+
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