[English] 日本語
Yorodumi
- PDB-1q87: Crystal structure of the C-domain of the T.vaginalis Inr binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q87
TitleCrystal structure of the C-domain of the T.vaginalis Inr binding protein, IBP39 (tetragonal form)
Components39 kDa initiator binding protein
KeywordsDNA BINDING PROTEIN / Initiator / Inr / Initiator binding protein / core promoter
Function / homologyInitiator binding domain / Initiator binding protein 39kDa, C-terminal / IBP39, C-terminal domain superfamily / Transcription-initiator DNA-binding domain IBD / Initiator binding protein 39 kDa / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / 39 kDa initiator binding protein
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsSchumacher, M.A. / Johnson, P.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structural Basis of Core Promoter Recognition in a Primitive Eukaryote
Authors: Schumacher, M.A. / Lau, A.O.T. / Johnson, P.J.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 39 kDa initiator binding protein
B: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)51,4542
Polymers51,4542
Non-polymers00
Water1,09961
1
A: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)25,7271
Polymers25,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)25,7271
Polymers25,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.420, 76.420, 157.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein 39 kDa initiator binding protein


Mass: 25727.221 Da / Num. of mol.: 2 / Fragment: C-domain, residues 127-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: ibp39 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95VR4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.23 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000, ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-50 mg/mlprotein1drop
2200 mMammonium sulfate1reservoir
350 mMMES1reservoirpH6.5
425 %PEG50001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.32→65 Å / Num. obs: 19164 / % possible obs: 91.6 % / Observed criterion σ(F): 11 / Observed criterion σ(I): 10.9 / Redundancy: 5.8 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.042
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / % possible all: 91.6
Reflection
*PLUS
Lowest resolution: 65 Å / Num. measured all: 111463

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q88, C-domain from the C2 monoclinic form

1q88


Resolution: 2.32→65 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1778869.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1891 9.9 %RANDOM
Rwork0.215 ---
all0.22 ---
obs0.215 19111 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.8645 Å2 / ksol: 0.351692 e/Å3
Displacement parametersBiso mean: 66.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.32 Å20 Å20 Å2
2---5.32 Å20 Å2
3---10.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.32→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 0 61 3115
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.05
LS refinement shellResolution: 2.32→2.47 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 238 10.5 %
Rwork0.309 2038 -
obs--66.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

+
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