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- PDB-2au3: Crystal Structure of the Aquifex aeolicus primase (Zinc Binding a... -

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Basic information

Entry
Database: PDB / ID: 2au3
TitleCrystal Structure of the Aquifex aeolicus primase (Zinc Binding and RNA Polymerase Domains)
ComponentsDNA primase
KeywordsTRANSFERASE / Zinc Ribbon / TOPRIM / RNA POLYMERASE / DNA REPLICATION
Function / homology
Function and homology information


DNA primase activity / primosome complex / DNA replication, synthesis of primer / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Pheromone ER-1 - #30 / DNA Primase; Chain A / Zinc finger, CHC2-type domain / DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / Pheromone ER-1 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Zinc finger, CHC2-type / DNA primase, DnaG ...Pheromone ER-1 - #30 / DNA Primase; Chain A / Zinc finger, CHC2-type domain / DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / Pheromone ER-1 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA Primase, CHC2-type zinc finger / DNA primase, catalytic core, N-terminal domain superfamily / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / TOPRIM / Toprim domain profile. / TOPRIM domain / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCorn, J.E. / Pease, P.J. / Hura, G.L. / Berger, J.M.
CitationJournal: Mol.Cell / Year: 2005
Title: Crosstalk between primase subunits can act to regulate primer synthesis in trans.
Authors: Corn, J.E. / Pease, P.J. / Hura, G.L. / Berger, J.M.
History
DepositionAug 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7572
Polymers46,6921
Non-polymers651
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.222, 66.403, 138.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA primase


Mass: 46691.512 Da / Num. of mol.: 1
Fragment: Zinc Binding and RNA Polymerase Domains (residues 1-405)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: dnaG / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+
References: UniProt: O67465, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: 18-22% EtOH, 55 mM HEPES, 100 mM NaCl, pH 7.5, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2003
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 27417 / Num. obs: 25989 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.45 % / Rsym value: 0.078 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2547 / Rsym value: 0.286 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Low-resolution Aquifex aeolicus DnaG from Tm-soak MAD

Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.516 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23826 1377 5 %RANDOM
Rwork0.20304 ---
all0.20488 25989 --
obs0.20488 25989 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2--1.9 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 1 169 3430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.994474
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022496
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21565
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1551.52004
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05523233
X-RAY DIFFRACTIONr_scbond_it2.88631321
X-RAY DIFFRACTIONr_scangle_it4.9574.51241
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.241 91
Rwork0.232 1757
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)
1-0.00060.2505-0.00841.34160.64471.5253-0.0194-0.154-0.0389-0.09370.02740.05120.10040.0539-0.0080.05030.02590.01070.18180.03420.095224.577112.43428.9399
20.26970.1028-0.00330.327-0.27140.8577-0.0195-0.08960.0575-0.03070.010.0362-0.0201-0.05220.00950.09440.0101-0.00260.1077-0.01020.11157.699326.742715.1694
31.61181.09760.6514.1591-0.86153.7114-0.16710.09550.1175-0.39150.20410.0241-0.13220.0057-0.0370.1444-0.05490.00340.04210.0440.096914.301450.348-10.7957
40000000000000000.1246000.124600.124614.64186.396222.3416
50.33960.13340.04320.0251-0.04830.3366-0.0099-0.05590.0294-0.06550.02440.01040.01130.0547-0.01450.11560.0251-0.00170.0995-0.01020.116712.84227.598813.5854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 943 - 96
2X-RAY DIFFRACTION2AA98 - 347100 - 349
3X-RAY DIFFRACTION3AA349 - 402351 - 404
4X-RAY DIFFRACTION4AB501
5X-RAY DIFFRACTION5AC502 - 670

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