[English] 日本語
Yorodumi
- PDB-9or6: Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9or6
TitleCrystal structure of PprA S-F-S tetramer from Deinococcus radiodurans
ComponentsDNA repair protein PprA
KeywordsDNA BINDING PROTEIN / PprA / Deinococcus / Deinococcus radiodurans / D. radiodurans / DNA repair / Genome reassembly / self-assembly / protein filament
Function / homologycellular response to desiccation / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-stranded DNA binding / damaged DNA binding / DNA repair / SPERMIDINE / DNA repair protein PprA
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSzabla, R. / Junop, M.S. / Wood, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2008R00075 Canada
CitationJournal: To Be Published
Title: Self-assembly of PprA from D.radiodurans
Authors: Szabla, R. / Junop, M.S.
History
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,8985
Polymers59,4622
Non-polymers4363
Water84747
1
A: DNA repair protein PprA
B: DNA repair protein PprA
hetero molecules

A: DNA repair protein PprA
B: DNA repair protein PprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,79610
Polymers118,9254
Non-polymers8716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)183.486, 34.083, 98.734
Angle α, β, γ (deg.)90.000, 98.337, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

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


Mass: 29731.230 Da / Num. of mol.: 2 / Mutation: D180K, D184K
Source method: isolated from a genetically manipulated source
Details: 1-8 deletion of PprA from D.radiodurans with D180K/D184K mutation
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: pprA, DR_A0346 / Plasmid: pMJ5666
Details (production host): pDEST-527-based expression plasmid
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32504
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: long and thin hexagonal-based prisms
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 1.5 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. | Protein solution: 5.0 mg/mL PprA (168 ...Details: 1.5 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. | Protein solution: 5.0 mg/mL PprA (168 uM), 43bp dsDNA (101 uM), 150mM KCl, 20mM Tris, pH 7.5, 1 mM MgCl2. | Crystallization solution (Molecular Dimensions - Morpheus 2 #94): 10 mM Spermine tetrahydrochloride, 10 mM Spermidine trihydrochloride, 10 mM 1,4 Diaminobutane dihydrochloride, 10 mM DL Ornithine monohydrochloride 0.1M Gly-Gly, AMPD, pH 8.5, 13% w/v PEG 4000, 21% w/v 1,2,6 Hexanetriol. | Well solution: 2.0 M Ammonium sulfate.
PH range: 7.5-8.5 / Temp details: Temperature-controlled incubator

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen cryo-stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2019 / Details: CMCF-ID optics setup
RadiationMonochromator: CMCF-ID default optics (Feb 2019) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9→90.774 Å / Num. obs: 13352 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 51.01 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.069 / Rrim(I) all: 0.13 / Net I/σ(I): 9.6
Reflection shellResolution: 2.904→2.954 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 633 / CC1/2: 0.756 / Rpim(I) all: 0.417 / Rrim(I) all: 0.61 / % possible all: 100

-
Processing

Software
NameVersionClassification
MxDCdata collection
autoPROC1.0.5 (20200206)data processing
XDSJan 31, 2020 (BUILT 20200131)data reduction
Aimless0.7.4data scaling
PHENIX1.21.2_5419phasing
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→90.77 Å / SU ML: 0.4166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 650 4.87 %
Rwork0.2266 12700 -
obs0.2276 13350 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.11 Å2
Refinement stepCycle: LAST / Resolution: 2.9→90.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 30 47 4070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374086
X-RAY DIFFRACTIONf_angle_d0.64165519
X-RAY DIFFRACTIONf_chiral_restr0.0428611
X-RAY DIFFRACTIONf_plane_restr0.0063729
X-RAY DIFFRACTIONf_dihedral_angle_d17.15931470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.130.33081410.27562572X-RAY DIFFRACTION99.89
3.13-3.430.34131270.27532527X-RAY DIFFRACTION99.36
3.46-3.940.27381120.23162209X-RAY DIFFRACTION88.69
3.94-4.970.20131370.20532650X-RAY DIFFRACTION99.57
4.97-90.770.21251330.20462742X-RAY DIFFRACTION99.52

+
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