[English] 日本語
Yorodumi
- PDB-1f36: THE CRYSTAL STRUCTURE OF FIS MUTANT K36E REVEALS THAT THE TRANSAC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f36
TitleTHE CRYSTAL STRUCTURE OF FIS MUTANT K36E REVEALS THAT THE TRANSACTIVATION REGION OF THE FIS PROTEIN CONTAINS EXTENDED MOBILE BETA-HAIRPIN ARMS
ComponentsFIS
KeywordsTRANSACTIVATION REGION / DNA-BINDING PROTEIN / PROTEIN-PROTEIN INTERACTION DOMAIN
Function / homology
Function and homology information


invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription activator activity / DNA-binding transcription repressor 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 activator activity / DNA-binding transcription repressor activity / chromosome organization / core promoter sequence-specific DNA binding / protein-DNA complex / response to radiation / 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-binding protein Fis
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSafo, M.K. / Yuan, H.S.
CitationJournal: EMBO J. / Year: 1997
Title: The transactivation region of the fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms.
Authors: Safo, M.K. / Yang, W.Z. / Corselli, L. / Cramton, S.E. / Yuan, H.S. / Johnson, R.C.
History
DepositionJun 20, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FIS
B: FIS


Theoretical massNumber of molelcules
Total (without water)22,5062
Polymers22,5062
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-34 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.900, 51.900, 294.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

-
Components

#1: Protein FIS


Mass: 11252.853 Da / Num. of mol.: 2 / Mutation: K36E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: YMEL / Cell line: BL21 / Gene: FIS / Plasmid: PRJ1296 / Cellular location (production host): NUCLEOID / Gene (production host): FIS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (-FIS) / References: UniProt: P0A6R3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.56 Å3/Da / Density % sol: 52 %
Description: SEARCH MODEL INCLUDED RESIDUES 24 - 98 OF THE DIMER AND THE CORRESPONDING TETRAPEPTIDE CHAINS (RESIDUES 10 - 13).
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.2
Details: CRYSTALS GROWN BY HANGING DROP VAPOR DIFFUSION FROM A SOLUTION OF 20 MG/ML PROTEIN, 500 MM NACL, 10 MM TRIS-HCL, PH 8.2, 2 M NAFORMATE, AGAINST 4 M NAFORMATE AS THE RESERVOIR, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22 Msodium formate1drop
34 Msodium formate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 16, 1996 / Details: Y
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 7139 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 1.63 / % possible all: 55.6
Reflection
*PLUS
Num. measured all: 79532
Reflection shell
*PLUS
% possible obs: 55.6 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
MSCdata reduction
MSCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ORTHORHOMBIC CRYSTAL FORM OF THE LYS36-GLU FIS STRUCTURE

Resolution: 2.65→8 Å / σ(F): 1
Details: MET A 1 - ASP A 9 ARE DISORDERED IN THE PROTEIN STRUCTURE. MET B 1 - ASP B 9 ARE DISORDERED IN THE PROTEIN STRUCTURE. PREVIOUSLY DISORDERED REGION (RESIDUES 1 - 24) IN ALL THE KNOWN CRYSTAL ...Details: MET A 1 - ASP A 9 ARE DISORDERED IN THE PROTEIN STRUCTURE. MET B 1 - ASP B 9 ARE DISORDERED IN THE PROTEIN STRUCTURE. PREVIOUSLY DISORDERED REGION (RESIDUES 1 - 24) IN ALL THE KNOWN CRYSTAL STRUCTERS OF THE FIS PROTEIN IS NOW PARTLY RESOLVED IN THIS LYS36-GLU FIS MUTANT (RESIDUES 10 - 24) AS BETA HAIRPIN STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 526 8 %RANDOM
Rwork0.222 ---
obs0.222 6577 90.6 %-
Displacement parametersBiso mean: 42.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 0 22 1438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.143
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)
11RESTRAINTX-RAY DIFFRACTION1
22X-RAY DIFFRACTION1
LS refinement shellResolution: 2.65→2.77 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.347 35 8 %
Rwork0.312 395 -
obs--50.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.13
LS refinement shell
*PLUS
Rfactor obs: 0.312

+
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