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- PDB-1uut: The Nuclease Domain of Adeno-Associated Virus Rep Complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1uut
TitleThe Nuclease Domain of Adeno-Associated Virus Rep Complexed with the RBE' Stemloop of the Viral Inverted Terminal Repeat
Components
  • 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'
  • REP PROTEIN
KeywordsHYDROLASE/DNA / NUCLEASE-COMPLEX / VIRAL PROTEIN / NUCLEASE / REPLICATION / PROTEIN-DNA / STEMLOOP / HELICASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


viral genome replication / endonuclease activity / DNA replication / hydrolase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDyda, F. / Hickman, A.B. / Ronning, D.R. / Perez, Z.N. / Kotin, R.M.
CitationJournal: 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.
History
DepositionJan 10, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REP PROTEIN
B: REP PROTEIN
C: 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'
D: 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8399
Polymers54,7064
Non-polymers1335
Water8,467470
1
A: REP PROTEIN
C: 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4616
Polymers27,3532
Non-polymers1084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: REP PROTEIN
D: 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3773
Polymers27,3532
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.830, 78.705, 184.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7938, -0.5824, 0.1755), (-0.6082, 0.7563, -0.2412), (0.0077, -0.2982, -0.9545)
Vector: 5.5113, 15.7642, 94.065)
DetailsTHE NUCLEASE DOMAIN OF THE REP PROTEIN HAS NO EVIDENCESHOWING OLIGOMERIZATION, AND MAY THEREFORE BE CONSIDEREDTO BE A MONOMER. IN THIS ENTRY, SINCE THE PROTEIN IS INCOMPLEX WITH DNA FROM THE INVERTED TERMINAL REPEATSEUENCES OF AAV-5 , THE COMPLEX IS ANNOTATED AS A DIMERICASSOCIATION .

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Components

#1: Protein REP PROTEIN


Mass: 22776.982 Da / Num. of mol.: 2 / Fragment: NUCLEASE DOMAIN, RESIDUES 1-197
Source method: isolated from a genetically manipulated source
Details: ALL RESIDUES ARE DELETED AFTER S197 / Source: (gene. exp.) ADENO-ASSOCIATED VIRUS 5 / Strain: SEROTYPE 5 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9YJC1
#2: DNA chain 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'


Mass: 4575.970 Da / Num. of mol.: 2 / Fragment: RBE STEMLOOP, RESIDUES 1-15 / Source method: obtained synthetically / Source: (synth.) ADENO-ASSOCIATED VIRUS 5
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1reservoirpH7.5
20.12 M1reservoirNaCl
30.2 Mmagnesium acetate1drop
40.1 Mcacodylate1droppH6.5
520 %(w/v)PEG80001drop

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 15, 2003 / Details: MULTILAYER MIRROR
RadiationMonochromator: MULTILAYER MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 38009 / % possible obs: 90 % / Redundancy: 4.2 % / Biso Wilson estimate: 25.02 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 3.8 / % possible all: 57
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 89.7 % / Num. measured all: 158265 / Rmerge(I) obs: 0.063

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M55

1m55


Resolution: 2→30 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1130 3 %RANDOM
Rwork0.195 ---
obs0.195 37161 88.1 %-
Displacement parametersBiso mean: 28.74 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 606 5 470 4265
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.298
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.012
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.194
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.232 92 3 %
Rwork0.264 2958 -
obs--58.57 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.012
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.194

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