[English] 日本語
Yorodumi
- PDB-1fym: SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fym
TitleSERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN A TAIL-TO-TAIL ORIENTATION
Components
  • HEAT SHOCK TRANSCRIPTION PROTEIN
  • TAIL-TO-TAIL HSE
KeywordsTRANSCRIPTION/DNA / crystal-packing interface / crystallization / protein-DNA interface / protein-protein interface / static disorder / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
Heat shock transcription factor family / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / heat shock factor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Heat shock transcription factor
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsLittlefield, O. / Nelson, H.C.M.
Citation
Journal: Proteins / Year: 2001
Title: Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex.
Authors: Littlefield, O. / Nelson, H.C.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: A New Use for the 'Wing' of the 'Winged' Helix-Turn-Helix Motif in the HSF-DNA Cocrystal
Authors: Littlefield, O. / Nelson, H.C.M.
History
DepositionOct 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Revision 1.4Nov 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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: TAIL-TO-TAIL HSE
D: TAIL-TO-TAIL HSE
A: HEAT SHOCK TRANSCRIPTION PROTEIN
B: HEAT SHOCK TRANSCRIPTION PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,2254
Polymers29,2254
Non-polymers00
Water1,65792
1
C: TAIL-TO-TAIL HSE

C: TAIL-TO-TAIL HSE

A: HEAT SHOCK TRANSCRIPTION PROTEIN

A: HEAT SHOCK TRANSCRIPTION PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,2254
Polymers29,2254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_545-x,y-1,-z1
2
D: TAIL-TO-TAIL HSE

D: TAIL-TO-TAIL HSE

B: HEAT SHOCK TRANSCRIPTION PROTEIN

B: HEAT SHOCK TRANSCRIPTION PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,2254
Polymers29,2254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+12
crystal symmetry operation2_546-x,y-1,-z+11
Unit cell
Length a, b, c (Å)106.510, 34.020, 78.210
Angle α, β, γ (deg.)90.00, 119.31, 90.00
Int Tables number5
Space group name H-MC121
Detailsprotein and DNA are not interacting in a physiologically relevant manner

-
Components

#1: DNA chain TAIL-TO-TAIL HSE


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is based on an idealized HSE sequence.
#2: Protein HEAT SHOCK TRANSCRIPTION PROTEIN / HEAT SHOCK TRANSCRIPTION FACTOR


Mass: 10950.279 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN / Mutation: N282R, F283H, K284A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Plasmid: PHN280R / Production host: Escherichia coli (E. coli) / References: UniProt: P22121
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, Isopropanol, Cacodylate, Ammonium Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Isopropanol11
3Cacodylate11
4Ammonium Acetate11
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
210 %isopropanol1reservoir
350 mMcacodylate1reservoir
4200 mMammonium acetate1reservoir
50.91 mMprotein1drop
60.69 mMDNA1drop
710 mMTris1drop
850 mM1dropNaCl
9400 mMammonium acetate1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.02
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 10644 / Num. obs: 10644 / % possible obs: 84.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.186 / % possible all: 72.7
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 72.7 % / Mean I/σ(I) obs: 4

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was originally refined by mistake with a glutamate at position 273. The deposited coordinates have been adjusted to contain aspartate at position 273, with the OD1 and OD2 ...Details: The structure was originally refined by mistake with a glutamate at position 273. The deposited coordinates have been adjusted to contain aspartate at position 273, with the OD1 and OD2 atoms having an arbitrary B-factor of 20.
RfactorNum. reflectionSelection details
Rfree0.295 1049 RANDOM
Rwork0.211 --
all-10642 -
obs-10642 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 486 0 92 1980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.388
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Rfactor Rfree: 0.372 / Num. reflection Rfree: 77 / Num. reflection Rwork: 733 / Rfactor obs: 0.29

+
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