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- PDB-6cbs: DnaG Primase C-terminal domain complex with SSB C-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 6cbs
TitleDnaG Primase C-terminal domain complex with SSB C-terminal peptide
ComponentsDNA primase, single-stranded DNA-binding protein chimera
KeywordsREPLICATION / Primase / DnaG / Single-strand DNA-Binding Protein / SSB / Complex
Function / homology
Function and homology information


DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA replication, synthesis of primer / replisome / replication fork processing / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / single-stranded DNA binding / DNA recombination ...DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA replication, synthesis of primer / replisome / replication fork processing / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal ...DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA primase, catalytic core, N-terminal domain superfamily / : / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / DNA Primase, CHC2-type zinc finger / Toprim-like / Single-stranded DNA-binding protein / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / TOPRIM / Toprim domain profile. / TOPRIM domain / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / Single-stranded DNA-binding protein / DNA primase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOakley, A.J. / Lo, A.T.Y.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP0877658 Australia
CitationJournal: To be Published
Title: DnaG Primase C-terminal domain complex with SSB C-terminal peptide
Authors: Oakley, A.J. / Lo, A.T.Y.
History
DepositionFeb 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA primase, single-stranded DNA-binding protein chimera
B: DNA primase, single-stranded DNA-binding protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,01512
Polymers37,3822
Non-polymers63310
Water7,476415
1
A: DNA primase, single-stranded DNA-binding protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0076
Polymers18,6911
Non-polymers3165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA primase, single-stranded DNA-binding protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0076
Polymers18,6911
Non-polymers3165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.895, 115.202, 45.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-533-

GLN

21B-533-

GLN

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Components

#1: Protein DNA primase, single-stranded DNA-binding protein chimera / DnaGC-SSB chimera


Mass: 18691.049 Da / Num. of mol.: 2
Fragment: DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12
Gene: dnaG, dnaP, parB, b3066, JW3038, ssb_1, BUE81_14300, ERS085374_00666
Plasmid: pAL1402 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0ABS5, UniProt: A0A0K3FKM0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953715 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953715 Å / Relative weight: 1
ReflectionResolution: 1.85→45 Å / Num. obs: 30129 / % possible obs: 93.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.326 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 15.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4449 / Rpim(I) all: 0.193 / Rrim(I) all: 0.503 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLM6.2.6data reduction
SCALA3.2.15data scaling
MOLREP9.4.09phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CBT

6cbt


Resolution: 1.85→42.574 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 1556 5.17 %RANDOM
Rwork0.1924 ---
obs0.194 30076 92.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→42.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 22 415 2654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042268
X-RAY DIFFRACTIONf_angle_d0.6413079
X-RAY DIFFRACTIONf_dihedral_angle_d5.2531654
X-RAY DIFFRACTIONf_chiral_restr0.036365
X-RAY DIFFRACTIONf_plane_restr0.004407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90970.32621300.27262641X-RAY DIFFRACTION96
1.9097-1.9780.2631330.24292637X-RAY DIFFRACTION97
1.978-2.05720.26081660.20092671X-RAY DIFFRACTION97
2.0572-2.15080.23891280.19522690X-RAY DIFFRACTION98
2.1508-2.26420.21741100.18932087X-RAY DIFFRACTION99
2.2642-2.40610.19831540.19472617X-RAY DIFFRACTION99
2.4061-2.59180.24891510.18682738X-RAY DIFFRACTION99
2.5918-2.85260.19681510.18482786X-RAY DIFFRACTION100
2.8526-3.26520.23931690.19012798X-RAY DIFFRACTION100
3.2652-4.11330.1971070.17411897X-RAY DIFFRACTION67
4.1133-42.5850.21471570.18712958X-RAY DIFFRACTION99
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)
11.8465-0.0966-0.29922.86730.41851.6311-0.15070.0114-0.2098-0.16190.0412-0.18590.19660.1120.05530.15980.01360.04560.13210.00430.12363.31541.88021.9275
24.20422.74550.54532.09250.18230.38460.01270.17440.0226-0.07610.06890.07210.1485-0.02020.01680.1841-0.0295-0.00540.1506-0.00410.1339-15.895942.17065.8976
33.39280.1721-1.85141.3484-0.47931.00820.08810.03070.0879-0.12430.04190.1223-0.12850.0842-0.03960.2231-0.0814-0.01950.1775-0.01140.0926-21.623840.40047.4616
42.0160.0338-0.00681.5961-0.14421.4456-0.09770.1737-0.2523-0.18280.0366-0.09130.23610.09050.04790.1705-0.01480.02510.1495-0.0670.16850.478898.124417.9536
51.0127-0.2439-0.15011.605-0.1052.017-0.11340.27-0.1495-0.37970.0014-0.67480.16540.26540.03040.1929-0.02020.10870.2796-0.0520.29039.7374101.636312.981
64.11613.83140.49694.45650.37450.7277-0.11540.25780.1919-0.05510.16750.24720.0799-0.1056-0.00940.1317-0.03520.02430.16880.00010.1264-13.6397100.399120.3522
72.14570.49731.12540.6195-0.58847.0085-0.22720.40060.052-0.83890.15430.83940.3545-0.38430.32610.5665-0.1927-0.07170.3237-0.23610.7755-31.234687.408120.5724
85.0337-0.8325-0.7686.60.51534.2136-0.03070.0479-0.20190.2753-0.32850.3264-0.29880.45470.37330.3121-0.14730.040.2551-0.02970.1806-25.557796.925327.0386
95.0403-1.7212-2.92552.93552.06665.15980.29520.6880.2824-0.4720.1453-0.2914-0.229-0.1222-0.45640.3522-0.0677-0.05140.2981-0.00290.2076-5.072103.4458.4354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 445 through 530 )
2X-RAY DIFFRACTION2chain 'A' and (resid 531 through 561 )
3X-RAY DIFFRACTION3chain 'A' and (resid 562 through 599 )
4X-RAY DIFFRACTION4chain 'B' and (resid 445 through 494 )
5X-RAY DIFFRACTION5chain 'B' and (resid 495 through 530 )
6X-RAY DIFFRACTION6chain 'B' and (resid 531 through 559 )
7X-RAY DIFFRACTION7chain 'B' and (resid 560 through 564 )
8X-RAY DIFFRACTION8chain 'B' and (resid 565 through 579 )
9X-RAY DIFFRACTION9chain 'B' and (resid 580 through 599 )

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