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- PDB-4im9: Cystal structure of DnaG primase C-terminal domain from Vibrio ch... -

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Basic information

Entry
Database: PDB / ID: 4im9
TitleCystal structure of DnaG primase C-terminal domain from Vibrio cholerae
ComponentsDNA primasePrimase
KeywordsTRANSFERASE / helicase-primase complex / DNA replication / Hair pin helix / helicase binding
Function / homologyDNAb Helicase; Chain A / DNAb Helicase; Chain A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsAbdul Rehman, S.A. / Tarique, K.F. / Gourinath, S.
CitationJournal: To be Published
Title: Cystal structure of DnaG primase C-terminal domain from Vibrio cholerae
Authors: Abdul Rehman, S.A. / Tarique, K.F. / Gourinath, S.
History
DepositionJan 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA primase
B: DNA primase
C: DNA primase


Theoretical massNumber of molelcules
Total (without water)53,1213
Polymers53,1213
Non-polymers00
Water77543
1
A: DNA primase


Theoretical massNumber of molelcules
Total (without water)17,7071
Polymers17,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA primase


Theoretical massNumber of molelcules
Total (without water)17,7071
Polymers17,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA primase


Theoretical massNumber of molelcules
Total (without water)17,7071
Polymers17,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.412, 73.779, 132.653
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 / Primase


Mass: 17706.951 Da / Num. of mol.: 3 / Fragment: Primase C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: C-terminal domain, dnaG, Primase, VC395_0535 / Plasmid: pET28(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3LX44, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium cacodylate trihydrate (pH 6.5), 0.2 M MgCl2, 30% W/v PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97872 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2012 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→66.326 Å / Num. all: 25083 / Num. obs: 25046 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1189 / % possible all: 98.3

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.46→66.326 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.048 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26369 1280 5.1 %RANDOM
Rwork0.22692 ---
obs0.22885 23822 99.8 %-
all-25083 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2---1.59 Å20 Å2
3---0.91 Å2
Refine analyzeLuzzati coordinate error obs: 0.3683 Å
Refinement stepCycle: LAST / Resolution: 2.46→66.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 0 43 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193293
X-RAY DIFFRACTIONr_angle_refined_deg1.5522.0014455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8325.29155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88215627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5461522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212410
LS refinement shellResolution: 2.457→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 84 -
Rwork0.298 1546 -
obs--97.49 %

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