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- PDB-3q36: Crystal structure of the 4Fe-4S cluster domain of human DNA prima... -

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Basic information

Entry
Database: PDB / ID: 3q36
TitleCrystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit
ComponentsDNA primase large subunit
KeywordsTRANSFERASE / pol alpha / primase / DNA replication / polymerase / iron-sulfur cluster / DNA-binding / dna-directed RNA polymerase / metal-binding / nucleotidyltransferase / phosphoprotein / primosome / transcription
Function / homology
Function and homology information


positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere ...positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / 4 iron, 4 sulfur cluster binding / DNA binding / nucleoplasm / metal ion binding
Similarity search - Function
DNA primase, large subunit, eukaryotic / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit
Similarity search - Domain/homology
: / IRON/SULFUR CLUSTER / DNA primase large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAgarkar, V.B. / Babayeva, N.D. / Tahirov, T.H.
CitationJournal: Cell Cycle / Year: 2011
Title: Crystal structure of the C-terminal domain of human DNA primase large subunit: Implications for the mechanism of the primase - polymerase alpha switch.
Authors: Agarkar, V.B. / Babayeva, N.D. / Pavlov, Y.I. / Tahirov, T.H.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / 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_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: DNA primase large subunit
B: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9285
Polymers44,1692
Non-polymers7593
Water37821
1
A: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4362
Polymers22,0841
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4923
Polymers22,0841
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.476, 83.724, 47.561
Angle α, β, γ (deg.)90.00, 97.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA primase large subunit / DNA primase 58 kDa subunit / p58


Mass: 22084.326 Da / Num. of mol.: 2 / Fragment: 4Fe-4S cluster domain (UNP residues 266-457)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate, 15% w/v PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 16851 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.1 / Num. unique all: 839 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LGB

3lgb


Resolution: 2.5→31.16 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2327525.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 813 4.9 %RANDOM
Rwork0.228 ---
obs0.228 16588 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3513 Å2 / ksol: 0.397363 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å21.19 Å2
2---0.19 Å20 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 17 21 2944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d1.95
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 133 5 %
Rwork0.325 2520 -
obs-2520 93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4sf4.parsf4.top
X-RAY DIFFRACTION5water_rep.paramwater.top

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