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- PDB-6dhw: Crystal structure of primase iron-sulfur domain (266-457) -

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Basic information

Entry
Database: PDB / ID: 6dhw
TitleCrystal structure of primase iron-sulfur domain (266-457)
ComponentsDNA primase large subunitPrimase
KeywordsREPLICATION / Iron sulfur cluster / DNA primase
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 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / 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 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / 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 / 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 / molecular replacement / Resolution: 2.013 Å
AuthorsHolt, M.E. / Salay, L.E. / Chazin, W.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118089 United States
CitationJournal: PLoS ONE / Year: 2018
Title: Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs.
Authors: Holt, M.E. / Salay, L.E. / O'Brien, E. / Barton, J.K. / Chazin, W.J.
History
DepositionMay 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,44810
Polymers44,1692
Non-polymers1,2808
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA primase large subunit
hetero molecules

A: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,44810
Polymers44,1692
Non-polymers1,2808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3920 Å2
ΔGint-143 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.193, 52.560, 88.774
Angle α, β, γ (deg.)90.000, 115.080, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 272 through 279 or resid 281...
21(chain B and (resid 272 through 279 or resid 281...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 272 through 279 or resid 281...A272 - 279
121(chain A and (resid 272 through 279 or resid 281...A281 - 289
131(chain A and (resid 272 through 279 or resid 281...A291 - 292
141(chain A and (resid 272 through 279 or resid 281...A294 - 301
151(chain A and (resid 272 through 279 or resid 281...A352
161(chain A and (resid 272 through 279 or resid 281...A270 - 457
171(chain A and (resid 272 through 279 or resid 281...A270 - 457
181(chain A and (resid 272 through 279 or resid 281...A270 - 457
191(chain A and (resid 272 through 279 or resid 281...A270 - 457
1101(chain A and (resid 272 through 279 or resid 281...A270 - 457
211(chain B and (resid 272 through 279 or resid 281...B272 - 279
221(chain B and (resid 272 through 279 or resid 281...B281 - 289
231(chain B and (resid 272 through 279 or resid 281...B291 - 292
241(chain B and (resid 272 through 279 or resid 281...B346 - 3
251(chain B and (resid 272 through 279 or resid 281...B272 - 457
261(chain B and (resid 272 through 279 or resid 281...B361 - 372
271(chain B and (resid 272 through 279 or resid 281...B379 - 39
281(chain B and (resid 272 through 279 or resid 281...B403 - 408
291(chain B and (resid 272 through 279 or resid 281...B403 - 408
2101(chain B and (resid 272 through 279 or resid 281...B410 - 429
2111(chain B and (resid 272 through 279 or resid 281...B0
2121(chain B and (resid 272 through 279 or resid 281...B441 - 459
2131(chain B and (resid 272 through 279 or resid 281...B441 - 450
2141(chain B and (resid 272 through 279 or resid 281...B452 - 457
2151(chain B and (resid 272 through 279 or resid 281...B500

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Components

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


Mass: 22084.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / 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 / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.64 Å3/Da / Density % sol: 53.33 % / Description: 2-dimensional plates
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM TRIS-HCl pH 8.5, 400 mM LiSO4, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 27613 / % possible obs: 90 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.88 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.072 / Rrim(I) all: 0.138 / Χ2: 0.952 / Net I/σ(I): 8.1 / Num. measured all: 99449
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.01-2.083.30.64826090.390.4140.7711.18886
2.08-2.173.40.42523420.8720.2680.5040.53276.5
2.17-2.263.60.45527610.7510.2780.5341.23190.8
2.26-2.383.70.3128840.9340.1870.3630.5995
2.38-2.533.70.22129070.9590.1330.2590.65894.6
2.53-2.733.70.22828640.1570.1470.2731.16594.3
2.73-33.70.10928480.9890.0660.1281.04493
3-3.443.70.08727910.9920.0530.1021.09290.5
3.44-4.333.60.06624990.8650.0420.0781.02580.5
4.33-503.70.0631080.9940.0360.070.97298.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.01 Å37.2 Å
Translation2.01 Å37.2 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
DENZOdata reduction
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L9Q

3l9q


Resolution: 2.013→37.197 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.99
Details: Omitted residues 315-360 of chains A and B in the molecular replacement model 3L9Q
RfactorNum. reflection% reflection
Rfree0.2113 1358 4.92 %
Rwork0.1806 --
obs0.1821 27584 89.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.64 Å2 / Biso mean: 38.8875 Å2 / Biso min: 15.52 Å2
Refinement stepCycle: final / Resolution: 2.013→37.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 46 107 2874
Biso mean--66.86 36.72 -
Num. residues----336
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1276X-RAY DIFFRACTION10.342TORSIONAL
12B1276X-RAY DIFFRACTION10.342TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0129-2.08480.23951190.23132415253484
2.0848-2.16830.2562980.20442243234176
2.1683-2.26690.2211390.20152635277491
2.2669-2.38640.24171560.19722722287895
2.3864-2.53590.23131440.1992768291295
2.5359-2.73170.22241450.19292723286894
2.7317-3.00640.23461380.19612713285193
3.0064-3.44120.2391560.18372650280691
3.4412-4.33450.18361080.15812394250280
4.3345-37.2030.1731550.15682963311899

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