[English] 日本語
Yorodumi
- PDB-1m7u: Crystal structure of a novel DNA-binding domain from Ndt80, a tra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m7u
TitleCrystal structure of a novel DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast
ComponentsNdt80 protein
KeywordsTRANSCRIPTION ACTIVATOR / yeast protein / DNA-binding / meiosis
Function / homology
Function and homology information


nuclear chromosome / meiotic cell cycle / sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / positive regulation of transcription by RNA polymerase II
Similarity search - Function
NDT80 DNA-binding domain / NDT80 DNA-binding domain / NDT80 DNA-binding domain superfamily / NDT80 / PhoG like DNA-binding family / NDT80 DNA-binding domain profile. / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Meiosis-specific transcription factor NDT80
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsMontano, S.P. / Cote, M.L. / Fingerman, I. / Pierce, M. / Vershon, A.K. / Georgiadis, M.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast
Authors: Montano, S.P. / Cote, M.L. / Fingerman, I. / Pierce, M. / Vershon, A.K. / Georgiadis, M.M.
History
DepositionJul 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE DISCREPANCIES ARE PRESENT DUE TO ERRORS IN PCR.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ndt80 protein
B: Ndt80 protein


Theoretical massNumber of molelcules
Total (without water)62,6152
Polymers62,6152
Non-polymers00
Water82946
1
A: Ndt80 protein


Theoretical massNumber of molelcules
Total (without water)31,3071
Polymers31,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ndt80 protein


Theoretical massNumber of molelcules
Total (without water)31,3071
Polymers31,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.960, 63.960, 285.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Ndt80 protein


Mass: 31307.455 Da / Num. of mol.: 2 / Fragment: DNA binding domain, residues 59-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Ndt80 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: P38830
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, citric acid, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 294 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.6 Mammonium sulfate1drop
20.1 Msodium citrate1droppH5.6
350 mMHEPES1droppH7.0
40.2 M1dropNaCl
51.6 Mammonium sulfate1reservoirpH5.6
6sodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jun 29, 2001
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 17541 / Num. obs: 17150 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39 Å2 / Rsym value: 0.067 / Net I/σ(I): 18.6
Reflection shellResolution: 2.8→2.86 Å / Mean I/σ(I) obs: 6.8 / Rsym value: 0.21 / % possible all: 89.9
Reflection
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Lowest resolution: 2.9 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 6.8

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflectionSelection details
Rfree0.29 885 RANDOM
Rwork0.232 --
all-17541 -
obs-17150 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 0 46 3793
LS refinement shellResolution: 2.8→2.86 Å /
RfactorNum. reflection
Rfree0.37 60
Rwork0.32 -
obs-955
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.43
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / Rfactor Rwork: 0.32

+
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