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- PDB-4mm2: Crystal structure of yeast primase catalytic subunit -

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Basic information

Entry
Database: PDB / ID: 4mm2
TitleCrystal structure of yeast primase catalytic subunit
ComponentsDNA primase small subunitPrimase
KeywordsREPLICATION / zinc finger
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
: / CITRIC ACID / DNA primase small subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPark, K.R. / An, J.Y. / Lee, Y. / Youn, H.S. / Lee, J.G. / Kang, J.Y. / Kim, T.G. / Lim, J.J. / Eom, S.H. / Wang, J.
CitationJournal: To be Published
Title: Crystal structure of yeast primase catalytic subunit
Authors: Park, K.R. / An, J.Y. / Lee, Y. / Youn, H.S. / Lee, J.G. / Kang, J.Y. / Kim, T.G. / Lim, J.J. / Eom, S.H. / Wang, J.
History
DepositionSep 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Database references / Refinement description
Category: refine / reflns ...refine / reflns / reflns_shell / struct_ref_seq_dif
Item: _refine.pdbx_starting_model / _reflns.pdbx_Rsym_value ..._refine.pdbx_starting_model / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.2Dec 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.3Nov 8, 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_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: DNA primase small subunit
B: DNA primase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,83614
Polymers96,3282
Non-polymers1,50812
Water7,116395
1
A: DNA primase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9187
Polymers48,1641
Non-polymers7546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA primase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9187
Polymers48,1641
Non-polymers7546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.370, 196.040, 53.960
Angle α, β, γ (deg.)90.00, 114.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 10 - 402 / Label seq-ID: 15 - 407

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein DNA primase small subunit / Primase / 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: 48163.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRI1, YIR008C, YIB8C / Plasmid: pETDuet vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10363, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 0.1M Na-Citrate, 0.2M NDSB, 5mM CdCl2, 30% PEG 600, 10mM ZnCl2 , pH 5.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.2826 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 111075 / Num. obs: 111075 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.17
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.988 / Mean I/σ(I) obs: 0.89 / Num. unique all: 5296 / % possible all: 59.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MHQ

4mhq


Resolution: 1.6→43.88 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.891 / SU B: 3.518 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29293 5568 5 %RANDOM
Rwork0.25496 ---
obs0.25689 105430 92.81 %-
all-111075 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.749 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.23 Å2
2---0.54 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 36 395 6941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196742
X-RAY DIFFRACTIONr_bond_other_d0.0040.026420
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9629124
X-RAY DIFFRACTIONr_angle_other_deg1.1513.00114817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1295808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87124.018341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.754151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1121551
X-RAY DIFFRACTIONr_chiral_restr0.0920.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217572
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021583
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24626 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 279 -
Rwork0.393 4987 -
obs--59.5 %

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