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- PDB-5xor: Crystal structure of N-terminal replicase protein of porcine circ... -

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Basic information

Entry
Database: PDB / ID: 5xor
TitleCrystal structure of N-terminal replicase protein of porcine circovirus type 2
ComponentsRep protein
KeywordsREPLICATION / PCV2 / Rep / Dimer
Function / homology
Function and homology information


DNA endonuclease activity, producing 5'-phosphomonoesters / nucleotidyltransferase activity / DNA replication / RNA helicase activity / nucleotide binding / host cell nucleus / DNA binding / RNA binding / metal ion binding
Similarity search - Function
Putative viral replication protein / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Replication-associated protein
Similarity search - Component
Biological speciesPorcine circovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsSong, Y. / Peng, G.
CitationJournal: J. Virol. / Year: 2018
Title: Crystal Structure of the Dimerized N Terminus of Porcine Circovirus Type 2 Replicase Protein Reveals a Novel Antiviral Interface
Authors: Luo, G. / Zhu, X. / Lv, Y. / Lv, B. / Fang, J. / Cao, S. / Chen, H. / Peng, G. / Song, Y.
History
DepositionMay 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rep protein
B: Rep protein
C: Rep protein
D: Rep protein
E: Rep protein


Theoretical massNumber of molelcules
Total (without water)90,3875
Polymers90,3875
Non-polymers00
Water1,15364
1
A: Rep protein
E: Rep protein


Theoretical massNumber of molelcules
Total (without water)36,1552
Polymers36,1552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rep protein
C: Rep protein


Theoretical massNumber of molelcules
Total (without water)36,1552
Polymers36,1552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Rep protein


Theoretical massNumber of molelcules
Total (without water)18,0771
Polymers18,0771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.932, 71.213, 131.718
Angle α, β, γ (deg.)90.00, 104.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Rep protein


Mass: 18077.359 Da / Num. of mol.: 5 / Fragment: UNP residues 1-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine circovirus 2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A9YPG7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1M HEPES sodium pH 8.0, 0.45 M sodium citrate tribasic dihydrate, 50% (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 46536 / % possible obs: 97.9 % / Redundancy: 4.4 % / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000V1.0data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hw0

2hw0


Resolution: 2.699→42.34 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.62 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2887 3764 9.66 %RANDOM
Rwork0.2243 ---
obs0.2306 38981 94.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.699→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 0 64 4107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014140
X-RAY DIFFRACTIONf_angle_d1.1545553
X-RAY DIFFRACTIONf_dihedral_angle_d4.0432495
X-RAY DIFFRACTIONf_chiral_restr0.05555
X-RAY DIFFRACTIONf_plane_restr0.007726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6992-2.73330.36831240.31391233X-RAY DIFFRACTION87
2.7333-2.76930.34471510.31111375X-RAY DIFFRACTION97
2.7693-2.80720.37861760.29731260X-RAY DIFFRACTION97
2.8072-2.84730.32721150.30551360X-RAY DIFFRACTION97
2.8473-2.88980.38171210.30831351X-RAY DIFFRACTION98
2.8898-2.9350.43631480.29551386X-RAY DIFFRACTION98
2.935-2.98310.37381600.2891296X-RAY DIFFRACTION98
2.9831-3.03450.35011240.28881333X-RAY DIFFRACTION98
3.0345-3.08960.33451620.26391410X-RAY DIFFRACTION97
3.0896-3.14910.38011410.25071272X-RAY DIFFRACTION97
3.1491-3.21330.32041360.26281343X-RAY DIFFRACTION97
3.2133-3.28320.32941460.25561354X-RAY DIFFRACTION97
3.2832-3.35950.38591390.25651301X-RAY DIFFRACTION96
3.3595-3.44350.37741630.24711331X-RAY DIFFRACTION96
3.4435-3.53650.27751390.24561303X-RAY DIFFRACTION95
3.5365-3.64050.28831210.21311306X-RAY DIFFRACTION96
3.6405-3.7580.28391570.22931282X-RAY DIFFRACTION95
3.758-3.89220.30121420.2211318X-RAY DIFFRACTION94
3.8922-4.04790.27681230.21411302X-RAY DIFFRACTION93
4.0479-4.2320.25021450.20261303X-RAY DIFFRACTION94
4.232-4.45490.25511370.18451275X-RAY DIFFRACTION94
4.4549-4.73370.26851320.16831266X-RAY DIFFRACTION92
4.7337-5.09860.19581270.17641286X-RAY DIFFRACTION92
5.0986-5.61060.25121370.21071231X-RAY DIFFRACTION92
5.6106-6.42010.29711440.20781279X-RAY DIFFRACTION93
6.4201-8.07940.24381380.21281278X-RAY DIFFRACTION93
8.0794-42.34530.19211160.17791183X-RAY DIFFRACTION85

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