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- PDB-4lil: Crystal structure of the catalytic subunit of human primase bound... -

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Basic information

Entry
Database: PDB / ID: 4lil
TitleCrystal structure of the catalytic subunit of human primase bound to UTP and Mn
ComponentsDNA primase small subunitPrimase
KeywordsTRANSFERASE / Prim fold
Function / homology
Function and homology information


DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / DNA primase activity ...DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / DNA primase activity / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / DNA replication initiation / Activation of the pre-replicative complex / Defective pyroptosis / magnesium ion binding / zinc ion binding / nucleoplasm / membrane
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
: / URIDINE 5'-TRIPHOSPHATE / DNA primase small subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVaithiyalingam, S. / Eichman, B.F. / Chazin, W.J.
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 11, 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 / 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_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.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_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)47,1315
Polymers46,4711
Non-polymers6594
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.346, 79.346, 148.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein DNA primase small subunit / Primase / DNA primase 49 kDa subunit / p49


Mass: 46471.223 Da / Num. of mol.: 1
Fragment: Catalytic subunit p48, UNP residues 1-390 (delta 360-379)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P49642, 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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M K/Na Tartrate and 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2012
RadiationMonochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15266 / Num. obs: 15266 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Rsym value: 0.76 / Net I/σ(I): 37.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.454 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.731 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 763 5.02 %
Rwork0.2136 --
obs0.2153 15205 99.9 %
all-15266 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→44.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 16 34 3163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113215
X-RAY DIFFRACTIONf_angle_d1.3274345
X-RAY DIFFRACTIONf_dihedral_angle_d15.5911211
X-RAY DIFFRACTIONf_chiral_restr0.092457
X-RAY DIFFRACTIONf_plane_restr0.006546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.80080.33261600.27142794X-RAY DIFFRACTION100
2.8008-3.08260.29951760.25562801X-RAY DIFFRACTION100
3.0826-3.52850.26941350.23192872X-RAY DIFFRACTION100
3.5285-4.44490.21851470.19262905X-RAY DIFFRACTION100
4.4449-44.73710.22551450.19853070X-RAY DIFFRACTION100
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)
13.0119-0.83-1.05672.2151-1.09533.76080.00290.26990.27630.1977-0.276-0.2184-0.55250.18460.14970.2924-0.0696-0.11220.30570.15280.369116.538675.58975.8255
21.8638-1.0373-0.16962.987-2.18813.8549-0.1320.2435-0.0892-0.0702-0.0923-0.06280.14830.03150.13820.325-0.0705-0.10760.31310.09280.334921.359656.757213.793
34.6298-0.58251.25355.0817-1.90624.396-0.22550.1603-1.0035-0.71690.53960.94230.9192-0.5175-0.10720.5212-0.1773-0.06750.36250.1120.529916.458231.795722.8852
43.6077-2.493-0.04962.4628-0.48392.9433-0.0697-0.0009-0.33280.1496-0.0404-0.1020.2876-0.23560.14180.3411-0.1534-0.05650.30690.11230.306513.29260.240314.9325
57.1011-1.05281.021.594-0.9370.3592-0.1902-1.2450.55710.69230.1151-0.282-0.7497-0.14310.10780.577-0.0323-0.08110.5190.0520.27969.012274.717222.6911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 301 )
4X-RAY DIFFRACTION4chain 'A' and (resid 302 through 349 )
5X-RAY DIFFRACTION5chain 'A' and (resid 350 through 404 )

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