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- PDB-4zo0: X-ray Structure of AAV-2 Origin Binding Domain -

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Basic information

Entry
Database: PDB / ID: 4zo0
TitleX-ray Structure of AAV-2 Origin Binding Domain
ComponentsProtein Rep68
KeywordsHYDROLASE / DNA binding protein / Adeno-Associated Virus / HUH nuclease
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
Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Rep protein catalytic-like / Rep protein catalytic domain like / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase ...Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Rep protein catalytic-like / Rep protein catalytic domain like / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Protein Rep68
Similarity search - Component
Biological speciesAdeno-associated virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMusayev, F.N. / Zarate-Perez, F. / Escalante, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM092854 United States
CitationJournal: Biochemistry / Year: 2015
Title: Structural Studies of AAV2 Rep68 Reveal a Partially Structured Linker and Compact Domain Conformation.
Authors: Musayev, F.N. / Zarate-Perez, F. / Bardelli, M. / Bishop, C. / Saniev, E.F. / Linden, R.M. / Henckaerts, E. / Escalante, C.R.
History
DepositionMay 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Rep68
B: Protein Rep68
C: Protein Rep68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6927
Polymers72,5593
Non-polymers1334
Water5,675315
1
A: Protein Rep68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2713
Polymers24,1861
Non-polymers842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein Rep68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2112
Polymers24,1861
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein Rep68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2112
Polymers24,1861
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)186.360, 154.400, 38.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-687-

HOH

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Components

#1: Protein Protein Rep68


Mass: 24186.441 Da / Num. of mol.: 3 / Fragment: Origin Binding Domain (UNP residues 1-206)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 2 (isolate Srivastava/1982)
Strain: isolate Srivastava/1982 / Gene: Rep68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P03132, DNA helicase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Isopropanol, Sodium acetate, Magnesium acetate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 50960 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 17.7
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 8.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M55

1m55


Resolution: 2.3→29.724 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 2545 4.99 %
Rwork0.2253 --
obs0.2261 50955 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 7 315 5028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0224836
X-RAY DIFFRACTIONf_angle_d1.4286595
X-RAY DIFFRACTIONf_dihedral_angle_d17.011737
X-RAY DIFFRACTIONf_chiral_restr0.157738
X-RAY DIFFRACTIONf_plane_restr0.011843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34420.34141380.27592577X-RAY DIFFRACTION99
2.3442-2.39210.30541550.24772634X-RAY DIFFRACTION100
2.3921-2.44410.28181330.24942702X-RAY DIFFRACTION100
2.4441-2.50090.28271330.25532620X-RAY DIFFRACTION100
2.5009-2.56340.26571350.24722670X-RAY DIFFRACTION100
2.5634-2.63270.29481560.24162633X-RAY DIFFRACTION100
2.6327-2.71010.25251230.25012666X-RAY DIFFRACTION100
2.7101-2.79750.28671350.25612698X-RAY DIFFRACTION100
2.7975-2.89740.24971350.25372642X-RAY DIFFRACTION100
2.8974-3.01330.25431570.2392676X-RAY DIFFRACTION100
3.0133-3.15030.22571610.242640X-RAY DIFFRACTION100
3.1503-3.31620.27391450.23542702X-RAY DIFFRACTION100
3.3162-3.52360.27411400.22842725X-RAY DIFFRACTION100
3.5236-3.79520.24551180.22872695X-RAY DIFFRACTION100
3.7952-4.17620.21861610.20742695X-RAY DIFFRACTION100
4.1762-4.77840.2261680.1852723X-RAY DIFFRACTION100
4.7784-6.0120.18821210.20612789X-RAY DIFFRACTION100
6.012-29.72630.21851310.22442923X-RAY DIFFRACTION98

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