[English] 日本語
Yorodumi
- PDB-6bdu: Crystal structure of PprA from Deinococcus radiodurans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bdu
TitleCrystal structure of PprA from Deinococcus radiodurans
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN / DNA damage repair / Radiation induced / Genome segregation / Filment formation
Function / homologycellular response to desiccation / positive regulation of DNA ligation / cellular response to gamma radiation / double-stranded DNA binding / damaged DNA binding / DNA repair / DNA repair protein PprA
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSzabla, R. / Czerwinski, M. / Junop, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2008R00075 Canada
CitationJournal: To Be Published
Title: Crystal structure of PprA from Deinococcus radiodurans
Authors: Szabla, R. / Czerwinski, M. / Junop, M.S.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA repair protein PprA
B: DNA repair protein PprA


Theoretical massNumber of molelcules
Total (without water)67,2062
Polymers67,2062
Non-polymers00
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer interface was observed in crystal structure of PprA from D.radiodurans, D.peraridilitoris and D.deserti.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-8 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.629, 99.149, 116.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein DNA repair protein PprA / Pleiotropic protein promoting DNA repair


Mass: 33602.750 Da / Num. of mol.: 2 / Mutation: D180K, D184K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: pprA, DR_A0346 / Plasmid: pDEST-527 / Cell line (production host): B834(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: O32504
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.44 Å3/Da / Density % sol: 49.53 % / Description: square prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein at 2.4mg/mL in 150mM KCl, 20mM Tris, pH 7.5 was mixed in 1:1 volume ratio with a solution of 0.2 M Lithium Citrate Tribasic and 20 % (w/v) PEG 3350. The drop was suspended over 1.5M Ammonium sulfate.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→58.34 Å / Num. obs: 45262 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.061 / Rrim(I) all: 0.159 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3281 / CC1/2: 0.658 / Rpim(I) all: 0.662 / Rrim(I) all: 1.606

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.21 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34
RfactorNum. reflection% reflection
Rfree0.2357 2315 5.12 %
Rwork0.205 --
obs0.2065 45188 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→36.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 0 376 4446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054140
X-RAY DIFFRACTIONf_angle_d0.6885600
X-RAY DIFFRACTIONf_dihedral_angle_d20.6171488
X-RAY DIFFRACTIONf_chiral_restr0.048616
X-RAY DIFFRACTIONf_plane_restr0.004744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04090.32741350.30382510X-RAY DIFFRACTION100
2.0409-2.08520.32941310.27852456X-RAY DIFFRACTION100
2.0852-2.13370.3291140.26392501X-RAY DIFFRACTION100
2.1337-2.18710.32091510.24212492X-RAY DIFFRACTION100
2.1871-2.24620.31071230.24012498X-RAY DIFFRACTION100
2.2462-2.31230.29881240.24222481X-RAY DIFFRACTION100
2.3123-2.38690.28311420.23032485X-RAY DIFFRACTION100
2.3869-2.47220.25721420.23492511X-RAY DIFFRACTION100
2.4722-2.57120.28271400.22632489X-RAY DIFFRACTION100
2.5712-2.68810.29651330.24162512X-RAY DIFFRACTION100
2.6881-2.82980.27211630.23122495X-RAY DIFFRACTION100
2.8298-3.0070.27621390.21692513X-RAY DIFFRACTION100
3.007-3.23910.2881360.21082504X-RAY DIFFRACTION100
3.2391-3.56480.20691500.19912546X-RAY DIFFRACTION100
3.5648-4.080.18251190.17592574X-RAY DIFFRACTION100
4.08-5.1380.17381190.162605X-RAY DIFFRACTION100
5.138-36.21590.17651540.17982701X-RAY DIFFRACTION100

+
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://pdbjlvh1.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