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- PDB-4ehs: Crystal structure of Helicobacter pylori DnaG Primase C terminal ... -

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Basic information

Entry
Database: PDB / ID: 4ehs
TitleCrystal structure of Helicobacter pylori DnaG Primase C terminal domain
ComponentsDNA primase
KeywordsTRANSFERASE / primase / helicase binding domain
Function / homology
Function and homology information


DNA primase DnaG / DNA primase activity / primosome complex / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA primase DnaG, C-terminal helicase-binding domain / DnaG-primase C-terminal, helicase-binding domain / DNAb Helicase; Chain A / DNAb Helicase; Chain A / 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 ...DNA primase DnaG, C-terminal helicase-binding domain / DnaG-primase C-terminal, helicase-binding domain / DNAb Helicase; Chain A / DNAb Helicase; Chain A / 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 / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / DNA primase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsAbdul Rehman, S.A. / Gourinath, S.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Crystal structure and mode of helicase binding of the C-terminal domain of primase from Helicobacter pylori
Authors: Abdul Rehman, S.A. / Verma, V. / Mazumder, M. / Dhar, S.K. / Gourinath, S.
History
DepositionApr 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Derived calculations
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,8336
Polymers36,5202
Non-polymers3134
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-20 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.883, 61.455, 82.421
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: 18260.176 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP Residues 413-559
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26995 / Gene: dnaG, DnaG Primase, HP_0012 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P56064, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.82 Å3/Da / Density % sol: 32.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 5000 MME, NaCl, pH 7.4, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2010 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 24493 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 42.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.78-1.814.90.3323.8194.2
1.81-1.846.10.298199.7
1.84-1.886.60.2461100
1.88-1.926.70.2311100
1.92-1.966.80.1891100
1.96-26.80.1541100
2-2.056.90.1271100
2.05-2.116.80.1161100
2.11-2.176.90.0931100
2.17-2.246.90.0831100
2.24-2.326.90.0751100
2.32-2.426.90.0671100
2.42-2.536.90.0621100
2.53-2.666.90.0581100
2.66-2.836.90.0561100
2.83-3.046.90.0521100
3.04-3.356.80.0531100
3.35-3.836.70.0521100
3.83-4.836.80.0431100
4.83-506.80.035199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0072refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→49.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.919 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24929 1250 5.1 %RANDOM
Rwork0.19502 ---
obs0.19779 23200 99.59 %-
all-24598 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.766 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--1.06 Å20 Å2
3----0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2199 Å
Refinement stepCycle: LAST / Resolution: 1.78→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 16 213 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192039
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1842.0532724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73624.32181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63815417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4771512
X-RAY DIFFRACTIONr_chiral_restr0.1260.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211420
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4671.51248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.59821998
X-RAY DIFFRACTIONr_scbond_it4.3183812
X-RAY DIFFRACTIONr_scangle_it6.8554.5753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.778→1.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 80 -
Rwork0.263 1469 -
obs--94.28 %

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