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- PDB-3lgb: Crystal Structure of the Fe-S Domain of the yeast DNA primase -

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Basic information

Entry
Database: PDB / ID: 3lgb
TitleCrystal Structure of the Fe-S Domain of the yeast DNA primase
ComponentsDNA primase large subunitPrimase
KeywordsTRANSFERASE / DNA primase / Fe-S cluster / DNA-binding / DNA-directed RNA polymerase / Iron / Iron-sulfur / Metal-binding / Nucleotidyltransferase / Primosome
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 replication, synthesis of primer / DNA replication initiation / double-strand break repair ...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 replication, synthesis of primer / DNA replication initiation / double-strand break repair / nuclear envelope / 4 iron, 4 sulfur cluster binding / DNA replication / DNA binding / metal ion binding / nucleus
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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsSauguet, L. / Pellegrini, L.
CitationJournal: PLOS ONE / Year: 2010
Title: Shared Active Site Architecture between the Large Subunit of Eukaryotic Primase and DNA Photolyase
Authors: Sauguet, L. / Klinge, S. / Perera, R.L. / Maman, J.D. / Pellegrini, L.
History
DepositionJan 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Experimental preparation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)47,2899
Polymers45,8862
Non-polymers1,4037
Water8,935496
1
A: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7714
Polymers22,9431
Non-polymers8283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5185
Polymers22,9431
Non-polymers5754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.570, 86.570, 141.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA primase large subunit / Primase / DNA primase 58 kDa subunit / DNA polymerase alpha:primase complex p58 subunit / Pol alpha-primase ...DNA primase 58 kDa subunit / DNA polymerase alpha:primase complex p58 subunit / Pol alpha-primase complex p58 subunit / DNA polymerase-primase complex p58 subunit


Mass: 22943.127 Da / Num. of mol.: 2 / Fragment: Fe-S DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRI2, YKL045W, YKL258 / Plasmid: pRSF Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3)
References: UniProt: P20457, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 5 types, 503 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M TrisHCl pH 7.5, 1mM Zn acetate, 11% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9793 Å
DetectorDate: Jun 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.54→29.34 Å / Num. obs: 88345 / % possible obs: 100 % / Redundancy: 22.4 % / Biso Wilson estimate: 18.88 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 21.6
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 4.4 / Num. unique all: 12872 / Rsym value: 0.778 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SOLVEphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.54→29.34 Å / Cor.coef. Fo:Fc: 0.9632 / Cor.coef. Fo:Fc free: 0.9629 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1643 4430 5.02 %RANDOM
Rwork0.1542 ---
obs0.1547 88274 100 %-
all-88274 --
Displacement parametersBiso mean: 26.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.1548 Å20 Å20 Å2
2---1.1548 Å20 Å2
3---2.3096 Å2
Refine analyzeLuzzati coordinate error obs: 0.155 Å
Refinement stepCycle: LAST / Resolution: 1.54→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3091 0 54 496 3641
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013304HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.934478HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1225SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes483HARMONIC5
X-RAY DIFFRACTIONt_it3304HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion15.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4322SEMIHARMONIC4
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1874 350 5.52 %
Rwork0.1759 5988 -
all0.1765 6338 -
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)
10.5064-0.2177-0.4681.35780.71431.4288-0.034-0.0139-0.01820.1010.0522-0.05770.0283-0.0065-0.0182-0.0332-0.00130.0026-0.058-0.0052-0.054724.23154.3916.6716
21.13140.5507-0.8310.6848-0.79341.0921-0.00650.01690.01470.11090.09280.062-0.0524-0.0945-0.0863-0.0097-0.00030.0121-0.04230.0221-0.038332.477834.0622-0.0666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A316 - 511
2X-RAY DIFFRACTION2B317 - 512

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