[English] 日本語
Yorodumi
- PDB-3eiv: Crystal Structure of Single-stranded DNA-binding protein from Str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eiv
TitleCrystal Structure of Single-stranded DNA-binding protein from Streptomyces coelicolor
ComponentsSingle-stranded DNA-binding protein 2
KeywordsDNA BINDING PROTEIN / Single-stranded DNA-binding protein / Streptomyces Coelicolor / DNA damage / DNA repair / DNA replication / DNA-binding / Phosphoprotein
Function / homology
Function and homology information


nucleoid / enzyme activator activity / single-stranded DNA binding / DNA replication / cytoplasm
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 2
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / molecular replacement / Resolution: 2.141 Å
AuthorsLuic, M. / Stefanic, Z. / Vujaklija, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the single-stranded DNA-binding protein from Streptomyces coelicolor.
Authors: Stefanic, Z. / Vujaklija, D. / Luic, M.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 2
B: Single-stranded DNA-binding protein 2
C: Single-stranded DNA-binding protein 2
D: Single-stranded DNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)79,7024
Polymers79,7024
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-44 kcal/mol
Surface area20450 Å2
MethodPISA
2
A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)39,8512
Polymers39,8512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-16 kcal/mol
Surface area11910 Å2
MethodPISA
3
C: Single-stranded DNA-binding protein 2
D: Single-stranded DNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)39,8512
Polymers39,8512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-14 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.454, 104.788, 163.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-213-

HOH

21B-259-

HOH

31C-294-

HOH

41D-217-

HOH

51D-231-

HOH

DetailsBiological unit is a tetramer. Biological unit is the same as asym. unit

-
Components

#1: Protein
Single-stranded DNA-binding protein 2 / SSB 2 / Helix-destabilizing protein 2


Mass: 19925.531 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor (bacteria) / References: UniProt: Q9X8U3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM TRIS-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.14→32.2 Å / Num. all: 48150 / Num. obs: 31640 / % possible obs: 65.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.44 % / Biso Wilson estimate: 48.39 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.0739 / Net I/σ(I): 13.373
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / Num. measured all: 22946 / Num. unique all: 5720 / Rsym value: 0.41 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.2 Å
Translation2.5 Å32.2 Å

-
Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-3000data collection
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: PDB ENTRY 1X3E

1x3e


Resolution: 2.141→31.182 Å / FOM work R set: 0.772 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2437 5.07 %RANDOM
Rwork0.23 ---
obs0.232 27266 99.73 %-
all-44287 --
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.116 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 90.21 Å2 / Biso mean: 46.76 Å2 / Biso min: 24.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.461 Å20 Å2-0 Å2
2--12.193 Å20 Å2
3----14.655 Å2
Refinement stepCycle: LAST / Resolution: 2.141→31.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 0 288 3438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.915

+
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