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

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Basic information

Entry
Database: PDB / ID: 6cbr
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 primase activity / DNA replication, synthesis of primer / replisome / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / single-stranded DNA binding ...DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / replisome / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / 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, 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-like / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / Single-stranded DNA-binding protein / 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
Single-stranded DNA-binding protein / DNA primase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 / 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

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


Theoretical massNumber of molelcules
Total (without water)37,3822
Polymers37,3822
Non-polymers00
Water5,567309
1
A: DNA primase,single-stranded DNA-binding protein chimera


Theoretical massNumber of molelcules
Total (without water)18,6911
Polymers18,6911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA primase,single-stranded DNA-binding protein chimera


Theoretical massNumber of molelcules
Total (without water)18,6911
Polymers18,6911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.723, 47.363, 51.881
Angle α, β, γ (deg.)63.51, 76.97, 73.81
Int Tables number1
Space group name H-MP1

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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 131-139)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 1.78 Å3/Da / Density % sol: 30.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 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: 0.95368 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
ReflectionResolution: 1.5→45 Å / Num. obs: 41299 / % possible obs: 90 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.649 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.039 / Net I/σ(I): 13.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5369 / Rpim(I) all: 0.275 / Rrim(I) all: 0.389 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLM6.2.6data reduction
SCALA3.2.25data scaling
MOLREP9.4.09phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1T3W

1t3w


Resolution: 1.5→41.496 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 19.09
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 1873 5.04 %RANDOM
Rwork0.1617 ---
obs0.1625 37157 89.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 0 309 2568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072297
X-RAY DIFFRACTIONf_angle_d0.8923120
X-RAY DIFFRACTIONf_dihedral_angle_d9.1211702
X-RAY DIFFRACTIONf_chiral_restr0.052371
X-RAY DIFFRACTIONf_plane_restr0.006408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54060.26551540.24712667X-RAY DIFFRACTION89
1.5406-1.58590.2311450.21322693X-RAY DIFFRACTION88
1.5859-1.63710.23161440.19522645X-RAY DIFFRACTION89
1.6371-1.69560.19961510.18432669X-RAY DIFFRACTION89
1.6956-1.76350.22461560.1752697X-RAY DIFFRACTION89
1.7635-1.84370.19541410.16472670X-RAY DIFFRACTION89
1.8437-1.9410.19571450.15822722X-RAY DIFFRACTION90
1.941-2.06260.18571400.15622723X-RAY DIFFRACTION90
2.0626-2.22180.18171340.14452721X-RAY DIFFRACTION90
2.2218-2.44540.15731470.15292775X-RAY DIFFRACTION91
2.4454-2.79920.18971200.16182741X-RAY DIFFRACTION91
2.7992-3.52630.16641610.15312758X-RAY DIFFRACTION91
3.5263-41.5120.14671350.15342803X-RAY DIFFRACTION93
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)
10.8811-0.4702-0.13511.25830.04381.5775-0.0285-0.0566-0.01460.10170.02850.0496-0.1049-0.04840.02260.083-0.0038-0.00240.08980.00470.0953-1.77245.5783-6.135
29.9006-5.3995-7.16732.96043.88815.1962-0.0786-0.01110.1724-0.0784-0.0727-0.0548-0.01230.0042-0.01510.09440.0168-0.0170.1807-0.04510.176811.204911.002-4.713
31.40870.5664-1.94640.6092-1.32673.1832-0.061-0.12-0.02480.06340.06340.09670.12450.11350.04730.1286-0.00190.01660.12010.00390.12410.9571-5.10718.3283
40.1722-0.57140.30121.996-1.18730.8947-0.0432-0.03570.0087-0.0235-0.1038-0.2914-0.0322-0.04630.08870.17120.01790.02490.13730.00950.1615-0.9104-10.084414.4229
55.0753-2.47140.30845.6537-1.55042.4962-0.06890.0974-0.1722-0.058-0.0214-0.46080.23290.4064-0.04050.15760.04680.04280.2679-0.00930.214934.62910.957316.0313
60.6808-0.1536-0.22760.4193-0.00210.84390.06130.0789-0.0342-0.1162-0.03670.0090.01720.0904-0.00410.0926-0.0071-0.00170.09-0.00070.103124.057214.710224.4081
70.3310.24770.06871.98082.85644.46840.15410.3699-0.0396-0.3758-0.24430.3310.1288-0.42750.05380.17310.0344-0.0770.2339-0.02740.132712.090917.575815.68
81.1131-0.1588-1.19390.82650.412.9394-0.11340.2385-0.1535-0.2671-0.12650.18310.2572-0.3170.00340.1435-0.0151-0.02190.1304-0.02860.117615.807910.902319.0224
90.5922-0.111-0.61720.80570.38381.0789-0.11640.0445-0.0412-0.1271-0.0338-0.01140.3364-0.01290.02340.18680.00680.01490.10140.00450.107922.35683.034826.6042
100.0286-0.398-0.40536.57656.85677.1531-0.0206-0.0012-0.1917-0.1691-0.0737-0.15530.22290.1473-0.07120.1374-0.00660.01720.1515-0.02350.175233.458715.043227.4155
110.22160.04691.17520.1901-0.0394.3047-0.0009-0.01450.004-0.0919-0.02230.0125-0.05680.02190.01740.13040.0093-0.0060.13380.00250.106722.033721.89139.66
121.8060.71210.45052.84161.01792.1010.0779-0.0842-0.15290.14950.0026-0.00860.0088-0.0854-0.00290.17720.0333-0.02170.1140.0090.135515.406929.3923-3.4973
130.44630.4564-0.06213.7896-0.97041.2186-0.09470.0705-0.0548-0.2029-0.1341-0.34160.26970.14040.0760.29280.08970.04430.1990.01120.15228.97417.504212.3343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 443 through 521 )
2X-RAY DIFFRACTION2chain 'A' and (resid 522 through 527 )
3X-RAY DIFFRACTION3chain 'A' and (resid 528 through 561 )
4X-RAY DIFFRACTION4chain 'A' and (resid 562 through 599 )
5X-RAY DIFFRACTION5chain 'B' and (resid 445 through 449 )
6X-RAY DIFFRACTION6chain 'B' and (resid 450 through 467 )
7X-RAY DIFFRACTION7chain 'B' and (resid 468 through 475 )
8X-RAY DIFFRACTION8chain 'B' and (resid 476 through 495 )
9X-RAY DIFFRACTION9chain 'B' and (resid 496 through 521 )
10X-RAY DIFFRACTION10chain 'B' and (resid 522 through 527 )
11X-RAY DIFFRACTION11chain 'B' and (resid 528 through 560 )
12X-RAY DIFFRACTION12chain 'B' and (resid 561 through 578 )
13X-RAY DIFFRACTION13chain 'B' and (resid 579 through 599 )

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