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- PDB-5z51: Helicase binding domain of primase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5z51
TitleHelicase binding domain of primase from Mycobacterium tuberculosis
Components(DNA primase) x 2
KeywordsTRANSFERASE / Helicase binding domain of primase / DNA REPLICATION / Primer synthesis
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 / plasma membrane / cytoplasm
Similarity search - Function
DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Toprim domain / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria ...DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Toprim domain / 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 / Toprim domain profile. / TOPRIM domain
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / DNA primase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.583 Å
AuthorsSharma, D.P. / Gourinath, S.
CitationJournal: Biochem. J. / Year: 2018
Title: Structural insights into the interaction of helicase and primase inMycobacterium tuberculosis.
Authors: Sharma, D.P. / Vijayan, R. / Rehman, S.A.A. / Gourinath, S.
History
DepositionJan 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: DNA primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3494
Polymers26,1842
Non-polymers1652
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, Chain A (complete Primase- CTD) bound to Chain B (cleaved Primase-CTD)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-4 kcal/mol
Surface area12980 Å2
Unit cell
Length a, b, c (Å)48.282, 137.559, 36.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA primase


Mass: 17942.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: dnaG, Rv2343c, MTCY98.12c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WNW1, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein DNA primase


Mass: 8241.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: dnaG, Rv2343c, MTCY98.12c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WNW1, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: PEG 3350, magnesium acetate, mops

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Data collection

DiffractionMean temperature: 177 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.49→68.78 Å / Num. obs: 40035 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.044 / Rrim(I) all: 0.088 / Rsym value: 0.076 / Net I/σ(I): 19.667
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3.9 % / Rpim(I) all: 0.299 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.583→28.492 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 1523 4.82 %RANDOM
Rwork0.1814 ---
obs0.1827 31615 92.83 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 40.38 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.583→28.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 11 320 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171871
X-RAY DIFFRACTIONf_angle_d1.6412533
X-RAY DIFFRACTIONf_dihedral_angle_d15.18688
X-RAY DIFFRACTIONf_chiral_restr0.105279
X-RAY DIFFRACTIONf_plane_restr0.008331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5832-1.63430.23921070.18912357X-RAY DIFFRACTION82
1.6343-1.69270.25651350.18982418X-RAY DIFFRACTION84
1.6927-1.76050.28271110.19682527X-RAY DIFFRACTION87
1.7605-1.84060.21951250.19212640X-RAY DIFFRACTION90
1.8406-1.93760.27491330.21912628X-RAY DIFFRACTION91
1.9376-2.0590.22941650.1932767X-RAY DIFFRACTION96
2.059-2.21790.22181310.18152857X-RAY DIFFRACTION97
2.2179-2.4410.19791600.17462884X-RAY DIFFRACTION98
2.441-2.79390.18551570.16842919X-RAY DIFFRACTION99
2.7939-3.5190.1941470.17462980X-RAY DIFFRACTION99
3.519-28.49640.19361520.17893115X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 42.1506 Å / Origin y: 45.1289 Å / Origin z: 16.1581 Å
111213212223313233
T0.0223 Å2-0.001 Å20.0129 Å2-0.0402 Å2-0.0142 Å2--0.0338 Å2
L0.0813 °2-0.0912 °20.0354 °2-0.272 °2-0.029 °2--0.0738 °2
S-0.0013 Å °-0.0127 Å °-0.0178 Å °-0.0167 Å °0.0454 Å °-0.029 Å °-0.0178 Å °0.0037 Å °0.0455 Å °
Refinement TLS groupSelection details: all

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