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- PDB-1rz9: Crystal Structure of AAV Rep complexed with the Rep-binding sequence -

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Basic information

Entry
Database: PDB / ID: 1rz9
TitleCrystal Structure of AAV Rep complexed with the Rep-binding sequence
Components
  • (26-MER) x 2
  • Rep protein
KeywordsViral protein/DNA / Protein-DNA complex / Viral protein-DNA COMPLEX
Function / homology
Function and homology information


viral genome replication / endonuclease activity / DNA replication / host cell nucleus / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Rep protein catalytic-like / Rep protein catalytic domain like / Replication Protein E1; Chain: A, - #20 / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. ...Rep protein catalytic-like / Rep protein catalytic domain like / Replication Protein E1; Chain: A, - #20 / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / 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
DNA / DNA (> 10) / DNA binding trs helicase
Similarity search - Component
Biological speciesAdeno-associated virus - 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHickman, A.B. / Ronning, D.R. / Perez, Z.N. / Kotin, R.M. / Dyda, F.
Citation
Journal: Mol.Cell / Year: 2004
Title: The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces.
Authors: Hickman, A.B. / Ronning, D.R. / Perez, Z.N. / Kotin, R.M. / Dyda, F.
#1: Journal: Mol.Cell / Year: 2002
Title: Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep.
Authors: Hickman, A.B. / Ronning, D.R. / Kotin, R.M. / Dyda, F.
History
DepositionDec 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

Downloads & links

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Assembly

Deposited unit
F: 26-MER
G: 26-MER
A: Rep protein
B: Rep protein
C: Rep protein
D: Rep protein
E: Rep protein


Theoretical massNumber of molelcules
Total (without water)129,8667
Polymers129,8667
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.671, 131.706, 82.164
Angle α, β, γ (deg.)90.00, 112.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 26-MER


Mass: 7939.062 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 26-MER


Mass: 8042.185 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein
Rep protein


Mass: 22776.982 Da / Num. of mol.: 5 / Fragment: AAV5 Rep Nuclease Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 5 / Genus: Dependovirus / Gene: rep / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9YJC1

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1reservoirpH7.5
20.12 M1reservoirNaCl
320 %(w/v)PEG30001drop
40.1 Msodium citrate1droppH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2003 / Details: mirrors
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 23530 / Observed criterion σ(I): -3 / Rsym value: 0.1 / Net I/σ(I): 6.2
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 3 / Mean I/σ(I) obs: 3 / Rsym value: 0.29 / % possible all: 74.7
Reflection
*PLUS
Highest resolution: 3.1 Å / Num. obs: 23005 / % possible obs: 87.8 % / Num. measured all: 72828 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M55

1m55


Resolution: 3.1→19.88 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 270093.95 / Data cutoff high rms absF: 270093.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1137 4.8 %RANDOM
Rwork0.286 ---
obs0.286 23530 84 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.191139 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.91 Å20 Å2-9.74 Å2
2--23.46 Å20 Å2
3----12.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7900 1060 0 0 8960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it1.432
X-RAY DIFFRACTIONc_scangle_it2.372.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 149 4.8 %
Rwork0.325 2956 -
obs--66.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å / Num. reflection obs: 22393 / Rfactor Rfree: 0.316 / Rfactor Rwork: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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