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- PDB-6o5l: Crystal structure of PprA filament from Deinococcus peraridilitoris -

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Basic information

Entry
Database: PDB / ID: 6o5l
TitleCrystal structure of PprA filament from Deinococcus peraridilitoris
ComponentsPprA
KeywordsDNA BINDING PROTEIN / DNA damage repair / radiation-induced / genome segregation / filament formation
Function / homologyDNA repair protein
Function and homology information
Biological speciesDeinococcus peraridilitoris
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSzabla, R. / Junop, M.S. / Rok, M.
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 filament from Deinococcus peraridilitoris
Authors: Szabla, R. / Czerwinski, M. / Junop, M.S.
History
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PprA


Theoretical massNumber of molelcules
Total (without water)34,7091
Polymers34,7091
Non-polymers00
Water00
1
A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA


  • defined by author
  • Evidence: homology, Both PprA-PprA interactions in this filament assembly have been observed previously in PprA from a different species of Deinococcus (D.radiodurans). PDB ID: 6A27 6A28 D. ...Evidence: homology, Both PprA-PprA interactions in this filament assembly have been observed previously in PprA from a different species of Deinococcus (D.radiodurans). PDB ID: 6A27 6A28 D.radiodurans PprA is known to form ordered filaments. DOI: doi: 10.1096/fj.201801506R
  • 417 kDa, 12 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)416,50312
Polymers416,50312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_555-y,x-y,z+1/31
crystal symmetry operation2_554-y,x-y,z-2/31
crystal symmetry operation3_555-x+y,-x,z+2/31
crystal symmetry operation3_554-x+y,-x,z-1/31
crystal symmetry operation10_555-y,-x,-z+1/31
crystal symmetry operation10_554-y,-x,-z-2/31
crystal symmetry operation11_555-x+y,y,-z1
crystal symmetry operation11_554-x+y,y,-z-11
crystal symmetry operation12_555x,x-y,-z+2/31
crystal symmetry operation12_554x,x-y,-z-1/31
2
A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA

A: PprA


Theoretical massNumber of molelcules
Total (without water)277,6698
Polymers277,6698
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation4_465-x-1,-y+1,z1
crystal symmetry operation8_565x-y,-y+1,-z1
crystal symmetry operation8_465x-y-1,-y+1,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
crystal symmetry operation11_355-x+y-2,y,-z1
Unit cell
Length a, b, c (Å)79.468, 79.468, 262.804
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein PprA


Mass: 34708.605 Da / Num. of mol.: 1 / Fragment: UNP residues 20-294 / Mutation: D192K, D196K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus peraridilitoris (strain DSM 19664 / LMG 22246 / CIP 109416 / KR-200) (bacteria)
Strain: DSM 19664 / LMG 22246 / CIP 109416 / KR-200 / Gene: Deipe_2275 / Plasmid: pDEST-527
Details (production host): Gateway cloning compatable vector. Adds an N-terminal hexahistidine tag (TEV protease-cleavable)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L0A1P5
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.7 % / Description: Hexagonal-based prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 54 uM protein, 5% w/v PEG8000, 500 mM sodium chloride, 75 mM imidazole, 10 mM Tris, 50 mM potassium phosphate, 10 mM trimethylamine-HCl
Temp details: temperature-controlled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.3→68.82 Å / Num. obs: 8106 / % possible obs: 100 % / Redundancy: 32.9 % / CC1/2: 0.999 / Rpim(I) all: 0.075 / Χ2: 1 / Net I/σ(I): 10.7
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 35.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1591 / CC1/2: 0.507 / Χ2: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLM7.2.2data reduction
PHASER(1.13_2998: ???)phasing
PHENIX(1.13_2998: ???)refinement
Aimless0.7.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MC8

6mc8


Resolution: 3.3→66.576 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.83 / Phase error: 32.5
RfactorNum. reflection% reflection
Rfree0.2986 639 4.57 %
Rwork0.2467 --
obs0.2489 8049 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→66.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 0 0 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082024
X-RAY DIFFRACTIONf_angle_d1.0592750
X-RAY DIFFRACTIONf_dihedral_angle_d12.51702
X-RAY DIFFRACTIONf_chiral_restr0.053313
X-RAY DIFFRACTIONf_plane_restr0.006369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3003-3.55510.40091350.36692633X-RAY DIFFRACTION100
3.5551-3.91290.36031340.3072667X-RAY DIFFRACTION100
3.9129-4.47890.30791070.26682693X-RAY DIFFRACTION100
4.4789-5.64250.27131370.23072656X-RAY DIFFRACTION100
5.6425-66.58980.26581260.20692681X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -6.219 Å / Origin y: 22.8399 Å / Origin z: 26.7447 Å
111213212223313233
T1.31 Å20.6991 Å20.2611 Å2-1.2557 Å20.4499 Å2--1.0463 Å2
L2.6373 °20.4153 °2-1.2166 °2-2.2649 °20.0302 °2--4.0669 °2
S-0.7805 Å °-1.8787 Å °-0.7608 Å °0.8464 Å °-0.0328 Å °-0.4357 Å °0.2431 Å °0.7289 Å °0.4962 Å °
Refinement TLS groupSelection details: all

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