[English] 日本語
Yorodumi
- PDB-2dud: Crystal structure of human mitochondrial single-stranded DNA-bind... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dud
TitleCrystal structure of human mitochondrial single-stranded DNA-binding protein(hmtSSB)
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / MITOCHONDRIA / SSB / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of mitochondrial DNA replication / positive regulation of helicase activity / mitochondrial DNA replication / DNA unwinding involved in DNA replication / mitochondrial nucleoid / Transcriptional activation of mitochondrial biogenesis / single-stranded DNA binding / protein homotetramerization / mitochondrial matrix / chromatin binding ...positive regulation of mitochondrial DNA replication / positive regulation of helicase activity / mitochondrial DNA replication / DNA unwinding involved in DNA replication / mitochondrial nucleoid / Transcriptional activation of mitochondrial biogenesis / single-stranded DNA binding / protein homotetramerization / mitochondrial matrix / chromatin binding / protein homodimerization activity / mitochondrion / RNA binding / extracellular exosome / identical protein binding / nucleus
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Single-stranded DNA-binding protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDong, X. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of human mitochondrial single-stranded DNA-binding protein(hmtSSB)
Authors: Dong, X. / Bessho, Y. / Shirouzu, M. / Yokoyama, S.
History
DepositionJul 21, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)30,7092
Polymers30,7092
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-2 kcal/mol
Surface area11090 Å2
MethodPISA
2
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein

A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)61,4174
Polymers61,4174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Buried area7170 Å2
ΔGint-13 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.900, 106.900, 90.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a dimer in the asymmetric

-
Components

#1: Protein Single-stranded DNA-binding protein / Mt-SSB / MtSSB / PWP1-interacting protein 17


Mass: 15354.269 Da / Num. of mol.: 2 / Fragment: Single-stranded DNA-binding protein, SSB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Plasmid: PX050223-18 / References: UniProt: Q04837

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: CHES, 0.2M NaCl, 10% PEG 8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2006
RadiationMonochromator: double flat Si (III) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8832 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 52.2 Å2 / Rsym value: 0.061 / Net I/σ(I): 68.4828
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 21.2 % / Mean I/σ(I) obs: 11.2 / Rsym value: 0.338 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S3O

1s3o


Resolution: 2.7→34.99 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1599585.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 445 5.1 %RANDOM
Rwork0.259 ---
obs0.259 8801 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8907 Å2 / ksol: 0.327667 e/Å3
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.47 Å27.92 Å20 Å2
2--4.47 Å20 Å2
3----8.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.7→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 0 0 1539
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.067
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg4.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d31
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.051.5
X-RAY DIFFRACTIONc_mcangle_it7.12
X-RAY DIFFRACTIONc_scbond_it8.072
X-RAY DIFFRACTIONc_scangle_it10.022.5
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.34 43 4 %
Rwork0.326 1028 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water.param

+
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