[English] 日本語
Yorodumi
- PDB-3vea: Crystal Structure of matP-matS23mer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vea
TitleCrystal Structure of matP-matS23mer
Components
  • 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'
  • 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'
  • Macrodomain Ter protein
KeywordsDNA BINDING PROTEIN/DNA / macrodomains / chromosome / DNA condensation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific DNA binding / cell division / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
MatP, N-terminal domain / Macrodomain Ter protein, MatP / MatP, N-terminal / MatP, C-terminal ribbon-helix-helix domain / MatP, N-terminal domain superfamily / MatP N-terminal domain / MatP C-terminal ribbon-helix-helix domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix ...MatP, N-terminal domain / Macrodomain Ter protein, MatP / MatP, N-terminal / MatP, C-terminal ribbon-helix-helix domain / MatP, N-terminal domain superfamily / MatP N-terminal domain / MatP C-terminal ribbon-helix-helix domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Macrodomain Ter protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSchumacher, M.A.
CitationJournal: Mol.Cell / Year: 2012
Title: Molecular basis for a protein-mediated DNA-bridging mechanism that functions in condensation of the E. coli chromosome.
Authors: Dupaigne, P. / Tonthat, N.K. / Espeli, O. / Whitfill, T. / Boccard, F. / Schumacher, M.A.
History
DepositionJan 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Macrodomain Ter protein
N: 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'
M: 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'
A: Macrodomain Ter protein


Theoretical massNumber of molelcules
Total (without water)50,0554
Polymers50,0554
Non-polymers00
Water1,11762
1
B: Macrodomain Ter protein
N: 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'
M: 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'
A: Macrodomain Ter protein

B: Macrodomain Ter protein
N: 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'
M: 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'
A: Macrodomain Ter protein


Theoretical massNumber of molelcules
Total (without water)100,1118
Polymers100,1118
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area24120 Å2
ΔGint-180 kcal/mol
Surface area44950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.980, 111.310, 169.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Macrodomain Ter protein / Matp


Mass: 17967.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: matP, y2737, YPO1433, YP_0877 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZG78
#2: DNA chain 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'


Mass: 7055.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: matS strand 2
#3: DNA chain 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*AP*CP*T)-3'


Mass: 7064.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: matS strand 1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG400, 0.1 M magnesium chloride, 0.1 M Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2011
RadiationMonochromator: KHOZU double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.55→34.87 Å / Num. all: 23120 / Num. obs: 20349 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 67.6 Å2
Reflection shellResolution: 2.55→2.78 Å / % possible all: 58

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EVB

3evb


Resolution: 2.55→34.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1819047.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1668 9.4 %RANDOM
Rwork0.222 ---
obs0.222 20295 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.2635 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 74.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.55→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 937 0 62 3487
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_mcbond_it4.771.5
X-RAY DIFFRACTIONc_mcangle_it6.712
X-RAY DIFFRACTIONc_scbond_it7.182
X-RAY DIFFRACTIONc_scangle_it9.142.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.442 178 8.9 %
Rwork0.406 1811 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

+
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