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- PDB-1ro2: Bifunctional DNA primase/polymerase domain of ORF904 from the arc... -

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Basic information

Entry
Database: PDB / ID: 1ro2
TitleBifunctional DNA primase/polymerase domain of ORF904 from the archaeal plasmid pRN1- Triple mutant F50M/L107M/L110M manganese soak
Componentshypothetical protein ORF904
KeywordsREPLICATION / DNA polymerase / primase / polymerization / evolution of nucleic acid polymerizing enzymes
Function / homology
Function and homology information


helicase activity / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Zinc stem-like domain / Prim-pol fold / Bifunctional DNA primase/polymerase domain / Bifunctional DNA primase/polymerase, N-terminal / DNA primase/polymerase, bifunctional, N-terminal / Primase helical domain / Bifunctional DNA primase/polymerase, N-terminal / Primase helical domain / Bifunctional DNA primase/polymerase, N-terminal / DNA primase, phage/plasmid ...Zinc stem-like domain / Prim-pol fold / Bifunctional DNA primase/polymerase domain / Bifunctional DNA primase/polymerase, N-terminal / DNA primase/polymerase, bifunctional, N-terminal / Primase helical domain / Bifunctional DNA primase/polymerase, N-terminal / Primase helical domain / Bifunctional DNA primase/polymerase, N-terminal / DNA primase, phage/plasmid / D5 N terminal like / Domain of unknown function DUF5906 / Family of unknown function (DUF5906) / DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / Signal recognition particle alu RNA binding heterodimer, srp9/1 / : / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / N-terminal domain of TfIIb / Single Sheet / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / SF3 helicase domain-containing protein
Similarity search - Component
Biological speciesSulfolobus islandicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLipps, G. / Weinzierl, A.O. / von Scheven, G. / Buchen, C. / Cramer, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structure of a bifunctional DNA primase-polymerase
Authors: Lipps, G. / Weinzierl, A.O. / Von Scheven, G. / Buchen, C. / Cramer, P.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Residue CYS A 196 and Residue PRO A 197 are not linked. The length of the C-N bond is 1.78.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein ORF904
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2964
Polymers25,1101
Non-polymers1863
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.811, 119.907, 41.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein hypothetical protein ORF904


Mass: 25109.846 Da / Num. of mol.: 1 / Mutation: F50M/L107M/L110M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q54324
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris, sodium acetate, PEG 4000, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
1100 mMTris-Cl1reservoirpH8.5
2200 mMsodium acetate1reservoir
330 %(w/v)PEG40001reservoir
45 mMdithiothreitol1reservoir
510 mMHEPES1droppH7.5
6150 mM1dropNaCl
73 mMdithiothreitol1drop
825 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.005, 0.9793, 1.280, 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2003
RadiationProtocol: MULTIPLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0051
20.97931
31.281
40.97971
ReflectionResolution: 1.6→20 Å / Num. obs: 31761 / % possible obs: 98.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.234 / % possible all: 86.6
Reflection shell
*PLUS
% possible obs: 86.6 % / Num. unique obs: 2752

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: Friedel pairs were used in the refinement.
RfactorNum. reflectionSelection details
Rfree0.2645 1714 random
Rwork0.2522 --
all-58318 -
obs-31761 -
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 3 213 1919
Refinement
*PLUS
Rfactor Rfree: 0.265 / Rfactor Rwork: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.63

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