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- PDB-8xms: Crystal structure of Porcine Circovirus type II Rep ATPase domain -

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Basic information

Entry
Database: PDB / ID: 8xms
TitleCrystal structure of Porcine Circovirus type II Rep ATPase domain
ComponentsReplication-associated protein
KeywordsVIRAL PROTEIN / Replication / ATPase / Viral protein.
Function / homology
Function and homology information


rolling circle single-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / endonuclease activity / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity ...rolling circle single-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / endonuclease activity / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Putative viral replication protein / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replication-associated protein
Similarity search - Component
Biological speciesPorcine circovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGuan, S.Y. / Song, Y.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972658 China
CitationJournal: J.Gen.Virol. / Year: 2024
Title: Crystal structure of the ATPase domain of porcine circovirus type 2 Rep protein.
Authors: Guan, S. / Li, Z. / Han, Y. / Tian, A. / Zhou, S. / Chen, H. / Peng, G. / Song, Y.
History
DepositionDec 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication-associated protein
B: Replication-associated protein
C: Replication-associated protein
D: Replication-associated protein
E: Replication-associated protein
F: Replication-associated protein


Theoretical massNumber of molelcules
Total (without water)113,1136
Polymers113,1136
Non-polymers00
Water3,207178
1
A: Replication-associated protein


Theoretical massNumber of molelcules
Total (without water)18,8521
Polymers18,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replication-associated protein


Theoretical massNumber of molelcules
Total (without water)18,8521
Polymers18,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Replication-associated protein


Theoretical massNumber of molelcules
Total (without water)18,8521
Polymers18,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Replication-associated protein


Theoretical massNumber of molelcules
Total (without water)18,8521
Polymers18,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Replication-associated protein


Theoretical massNumber of molelcules
Total (without water)18,8521
Polymers18,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Replication-associated protein


Theoretical massNumber of molelcules
Total (without water)18,8521
Polymers18,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.920, 103.930, 76.850
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Replication-associated protein / ATP-dependent helicase Rep / RepP


Mass: 18852.090 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine circovirus 2 / Gene: Rep, ORF1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8BB16, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'- ...References: UniProt: Q8BB16, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-TRIS PH6.0, 0.2M Li2SO4, 22% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.95915 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jan 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95915 Å / Relative weight: 1
ReflectionResolution: 2.2→59.33 Å / Num. obs: 50956 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 4415 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→59.33 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.866 / SU B: 9.429 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31926 2491 4.9 %RANDOM
Rwork0.28924 ---
obs0.29073 48441 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.462 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.08 Å2
2--0.12 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.2→59.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6898 0 0 178 7076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0117248
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166528
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6629948
X-RAY DIFFRACTIONr_angle_other_deg0.51.58615072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2125858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.827542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.111101074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021734
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9664.1523450
X-RAY DIFFRACTIONr_mcbond_other4.9664.1523450
X-RAY DIFFRACTIONr_mcangle_it7.5957.4524302
X-RAY DIFFRACTIONr_mcangle_other7.5957.4524303
X-RAY DIFFRACTIONr_scbond_it5.7344.6723798
X-RAY DIFFRACTIONr_scbond_other5.7334.6723799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.878.3255647
X-RAY DIFFRACTIONr_long_range_B_refined13.80654.5629381
X-RAY DIFFRACTIONr_long_range_B_other13.80654.5629382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 189 -
Rwork0.313 3579 -
obs--100 %

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