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- PDB-1s9h: Crystal Structure of Adeno-associated virus Type 2 Rep40 -

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Basic information

Entry
Database: PDB / ID: 1s9h
TitleCrystal Structure of Adeno-associated virus Type 2 Rep40
ComponentsRep 40 protein
KeywordsREPLICATION / Helicase / AAA+ protein / P-loop / Walker A / Walker B / Sensor 1
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / viral DNA genome replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endonuclease activity / DNA helicase / DNA replication / host cell nucleus / ATP hydrolysis activity ...symbiont-mediated arrest of host cell cycle during G2/M transition / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / viral DNA genome replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endonuclease activity / DNA helicase / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #950 / Rep protein catalytic-like / : / Rep protein catalytic domain like / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #950 / Rep protein catalytic-like / : / Rep protein catalytic domain like / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesAdeno-associated virus - 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJames, J.A. / Escalante, C.R. / Yoon-Robarts, M. / Edwards, T.A. / Linden, R.M. / Aggarwal, A.K.
CitationJournal: Structure / Year: 2003
Title: Crystal Structure of the SF3 Helicase from Adeno-Associated Virus Type 2
Authors: James, J.A. / Escalante, C.R. / Yoon-Robarts, M. / Edwards, T.A. / Linden, R.M. / Aggarwal, A.K.
History
DepositionFeb 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rep 40 protein
B: Rep 40 protein
C: Rep 40 protein


Theoretical massNumber of molelcules
Total (without water)90,5953
Polymers90,5953
Non-polymers00
Water6,431357
1
A: Rep 40 protein


Theoretical massNumber of molelcules
Total (without water)30,1981
Polymers30,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rep 40 protein


Theoretical massNumber of molelcules
Total (without water)30,1981
Polymers30,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rep 40 protein


Theoretical massNumber of molelcules
Total (without water)30,1981
Polymers30,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.294, 126.294, 97.894
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Rep 40 protein / DNA replication protein / non-capsid protein


Mass: 30198.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 2 / Genus: Dependovirus / Gene: REP / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLySS / References: GenBank: 2906019, UniProt: P03132*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Sodium acetate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11091
21091
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C10.9812, 0.9810, 0.9583
SYNCHROTRONNSLS X6A20.9786
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
ADSC QUANTUM 42CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.98121
20.9811
30.95831
40.97861
ReflectionResolution: 2.4→50 Å / Num. all: 35212 / Num. obs: 35212 / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.059 / Net I/σ(I): 16.8
Reflection shellHighest resolution: 2.4 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.42 / % possible all: 84

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 186063.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2930 9.9 %RANDOM
Rwork0.227 ---
obs0.227 29685 85.5 %-
all-29685 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.6519 Å2 / ksol: 0.32412 e/Å3
Displacement parametersBiso mean: 51.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å28.43 Å20 Å2
2--1.03 Å20 Å2
3----2.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 0 357 5963
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 409 9.8 %
Rwork0.321 3779 -
obs--72.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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