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- PDB-4lim: Crystal structure of the catalytic subunit of yeast primase -

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Basic information

Entry
Database: PDB / ID: 4lim
TitleCrystal structure of the catalytic subunit of yeast primase
ComponentsDNA primase small subunit
KeywordsTRANSFERASE / Prim fold
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / DNA primase activity / DNA replication, synthesis of primer / nuclear replication fork ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / DNA primase activity / DNA replication, synthesis of primer / nuclear replication fork / DNA replication initiation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / ATP binding / metal ion binding
Similarity search - Function
DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, small subunit / DNA primase small subunit / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA primase small subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsVaithiyalingam, S. / Chazin, W.J. / Berger, J.M. / Corn, J. / Stephenson, S.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Insights into Eukaryotic Primer Synthesis from Structures of the p48 Subunit of Human DNA Primase.
Authors: Vaithiyalingam, S. / Arnett, D.R. / Aggarwal, A. / Eichman, B.F. / Fanning, E. / Chazin, W.J.
History
DepositionJul 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6712
Polymers45,6051
Non-polymers651
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.166, 43.624, 69.383
Angle α, β, γ (deg.)83.11, 83.25, 78.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA primase small subunit / DNA polymerase alpha:primase complex p48 subunit / DNA polymerase-primase complex p48 subunit / Pol ...DNA polymerase alpha:primase complex p48 subunit / DNA polymerase-primase complex p48 subunit / Pol alpha-primase complex p48 subunit / DNA primase 48 kDa subunit


Mass: 45605.129 Da / Num. of mol.: 1 / Fragment: UNP residues 8-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRI1, PRIM1, YIB8C, YIR008C / Production host: Escherichia coli (E. coli)
References: UniProt: P10363, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.38 Å3/Da / Density % sol: 48.41 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.6→19.8 Å / Num. all: 50009 / Num. obs: 50009 / % possible obs: 95.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.6 Å / % possible all: 95.12

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→19.8 Å / SU ML: 0.15 / σ(F): 2.01 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 2554 5.11 %
Rwork0.1548 --
obs0.1565 50009 95.12 %
all-50009 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 1 492 3617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193233
X-RAY DIFFRACTIONf_angle_d1.844374
X-RAY DIFFRACTIONf_dihedral_angle_d13.7291242
X-RAY DIFFRACTIONf_chiral_restr0.123463
X-RAY DIFFRACTIONf_plane_restr0.012567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.66140.19831190.19122368X-RAY DIFFRACTION84
1.6614-1.69530.22461350.18532534X-RAY DIFFRACTION92
1.6953-1.73210.21691370.17832575X-RAY DIFFRACTION93
1.7321-1.77240.19711600.17462621X-RAY DIFFRACTION95
1.7724-1.81670.18731350.16112604X-RAY DIFFRACTION95
1.8167-1.86580.21111440.16192640X-RAY DIFFRACTION95
1.8658-1.92060.18951380.16342618X-RAY DIFFRACTION95
1.9206-1.98250.19021640.16412662X-RAY DIFFRACTION96
1.9825-2.05330.18661330.15062650X-RAY DIFFRACTION96
2.0533-2.13550.17141520.15152648X-RAY DIFFRACTION96
2.1355-2.23250.191270.15322687X-RAY DIFFRACTION96
2.2325-2.350.20191330.15482703X-RAY DIFFRACTION96
2.35-2.4970.21991410.16292656X-RAY DIFFRACTION97
2.497-2.68940.21791500.16092712X-RAY DIFFRACTION97
2.6894-2.95920.2061550.16382656X-RAY DIFFRACTION97
2.9592-3.38560.19241480.15842758X-RAY DIFFRACTION98
3.3856-4.25850.16611280.13562707X-RAY DIFFRACTION98
4.2585-19.83040.16211550.14512656X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41650.37060.2262.79540.02521.7289-0.01270.12530.0918-0.24930.02510.1272-0.0115-0.0785-0.01840.11190.005-0.01650.11670.01730.08468.699310.760545.4126
21.00250.30450.51511.70610.04961.66580.0007-0.06680.04080.0711-0.0039-0.06970.0440.01830.00820.07310.02460.01160.1153-0.01570.128215.063110.63163.7935
31.8344-0.56781.07084.6488-1.47222.67440.1085-0.1868-0.05550.0515-0.1468-0.34660.2578-0.0840.02760.2689-0.04190.01280.31670.0150.123820.7484-0.1483.3226
42.32140.66850.65933.71590.59722.70270.334-0.3828-0.27990.7416-0.0288-0.24821.0052-0.2391-0.28860.579-0.0545-0.0970.44760.11170.262823.9025-11.133595.5791
50.25830.1040.27690.9119-0.36352.63730.0481-0.12180.0280.1768-0.093-0.04740.07830.1670.04520.12560.01590.01840.1733-0.00160.139116.69514.849671.9175
61.701-1.45630.23022.9518-0.34072.0570.1021-0.06420.04860.02470.0308-0.1021-0.0206-0.2505-0.09630.0750.00540.02620.19030.00890.1744-3.15897.946155.791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 251 )
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 289 )
5X-RAY DIFFRACTION5chain 'A' and (resid 290 through 347 )
6X-RAY DIFFRACTION6chain 'A' and (resid 348 through 393)

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