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- PDB-1m55: Catalytic domain of the Adeno Associated Virus type 5 Rep protein -

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Basic information

Entry
Database: PDB / ID: 1m55
TitleCatalytic domain of the Adeno Associated Virus type 5 Rep protein
ComponentsRep protein
KeywordsVIRAL PROTEIN / ENDONUCLEASE / REP / ROLLING CIRCLE REPLICATION / ADENO-ASSOCIATED VIRUS
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 binding trs helicase
Similarity search - Component
Biological speciesAdeno-associated virus - 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsHickman, A.B. / Ronning, D.R. / Kotin, R.M. / Dyda, F.
CitationJournal: 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
DepositionJul 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rep protein
B: Rep protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,01710
Polymers45,5542
Non-polymers4638
Water12,160675
1
A: Rep protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9434
Polymers22,7771
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rep protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0746
Polymers22,7771
Non-polymers2975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.888, 73.455, 65.560
Angle α, β, γ (deg.)90.0, 94.491, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rep protein / ADENO-ASSOCIATED VIRUS 5


Mass: 22776.982 Da / Num. of mol.: 2 / Fragment: Catalytic domain (Residues 1-197)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 5 / Genus: Dependovirus / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9YJC1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, PEG 400, ZINC ACETATE, SODIUM CACODYLATE, TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(v/v)PEG4001drop
280 mMsodium cacodylate1droppH6.5
324 mMzinc acetate1drop
410 %(v/v)PEG80001drop
5100 mMcacodylate1reservoir
630 mMzinc acetate1reservoir
712.5 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 6, 2001
RadiationMonochromator: Si(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 79390 / Num. obs: 79390 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.71 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 10
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.68 / Num. unique all: 4502 / Rsym value: 0.404 / % possible all: 95.9
Reflection
*PLUS
Num. measured all: 373647 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.404

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.196 1143 Random
Rwork0.178 --
all-77130 -
obs-77130 -
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 8 675 3843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.355
LS refinement shellResolution: 1.4→1.46 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.279 138 -
Rwork0.261 --
obs-8543 95.35 %
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.36
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / Rfactor Rwork: 0.261

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