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- PDB-1g71: CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS DNA PRIMASE -

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Basic information

Entry
Database: PDB / ID: 1g71
TitleCRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS DNA PRIMASE
ComponentsDNA PRIMASEPrimase
KeywordsREPLICATION / zinc-knuckle
Function / homology
Function and homology information


primosome complex / DNA primase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / metal ion binding
Similarity search - Function
DNA primase S; domain 2 / DNA primase small subunit PriS / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, small subunit / DNA primase small subunit / Helicase, Ruva Protein; domain 3 / Alpha-Beta Complex / Orthogonal Bundle ...DNA primase S; domain 2 / DNA primase small subunit PriS / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, small subunit / DNA primase small subunit / Helicase, Ruva Protein; domain 3 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA primase small subunit PriS
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.3 Å
AuthorsAugustin, M.A. / Huber, R. / Kaiser, J.T.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of a DNA-dependent RNA polymerase (DNA primase).
Authors: Augustin, M.A. / Huber, R. / Kaiser, J.T.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: DNA PRIMASE
B: DNA PRIMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,41014
Polymers81,6822
Non-polymers72812
Water6,089338
1
A: DNA PRIMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2057
Polymers40,8411
Non-polymers3646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA PRIMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2057
Polymers40,8411
Non-polymers3646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.883, 136.326, 61.877
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 DNA PRIMASE / Primase


Mass: 40841.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET 22 B (+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 DE3 / References: UniProt: Q9P9H1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3.36 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1M Tris/Cl, 2M Ammoniumsulfate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-Cl1reservoirpH8.5
22 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→17.31 Å / Num. all: 49651 / Num. obs: 46200 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 4.6 / Num. unique all: 6179 / % possible all: 84.1
Reflection
*PLUS
% possible obs: 93 %
Reflection shell
*PLUS
% possible obs: 74.8 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 4646 9.4 %RANDOM
Rwork0.211 ---
all-49651 --
obs-46200 93 %-
Solvent computationSolvent model: bulk_solvent correction cns 1.0 / Bsol: 62.4884 Å2 / ksol: 0.38931 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.82 Å20 Å20 Å2
2---2.13 Å20 Å2
3----3.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 2.3→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 0 28 338 6070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009493
X-RAY DIFFRACTIONc_angle_deg1.4479
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.263 86 12.5 %
Rwork0.232 687 -
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 9.4 % / Rfactor obs: 0.2108
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.263 / % reflection Rfree: 12.5 % / Rfactor Rwork: 0.232

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