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- PDB-5w33: Crystal structure of the RNA polymerase domain (RPD) of Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 5w33
TitleCrystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG
ComponentsDNA primase
KeywordsDNA BINDING PROTEIN / DNA replication / replisome / TOPRIM fold / DNA binding
Function / homology
Function and homology information


DNA primase DnaG / primosome complex / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA binding / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / Toprim domain / 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 domain / DNA primase DNAg catalytic core, N-terminal domain / DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / Toprim domain / 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 / Toprim domain / Toprim domain profile. / TOPRIM domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHou, C. / Biswas, T. / Tsodikov, O.V.
CitationJournal: Biochemistry / Year: 2018
Title: Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events.
Authors: Hou, C. / Biswas, T. / Tsodikov, O.V.
History
DepositionJun 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
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

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Assembly

Deposited unit
A: DNA primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6433
Polymers35,4501
Non-polymers1922
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-23 kcal/mol
Surface area15560 Å2
2
A: DNA primase
hetero molecules

A: DNA primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2856
Polymers70,9012
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+2,y,-z1
Buried area2330 Å2
ΔGint-57 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.495, 117.495, 87.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein DNA primase


Mass: 35450.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: dnaG, Rv2343c, MTCY98.12c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WNW1, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.24 Å3/Da / Density % sol: 70.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.85 M ammonium sulfate, 50 mM Tris pH 8.5 and 5% v/v PEG 400, 1 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14758 / % possible obs: 99.2 % / Observed criterion σ(I): 1.9 / Redundancy: 4.4 % / Net I/σ(I): 18

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDE

1dde


Resolution: 2.85→35 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.212 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.512 / ESU R Free: 0.328 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27294 737 5 %RANDOM
Rwork0.2407 ---
obs0.2423 13944 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.13 Å2
Refinement stepCycle: 1 / Resolution: 2.85→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 10 9 2376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192408
X-RAY DIFFRACTIONr_bond_other_d0.0010.022304
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9613240
X-RAY DIFFRACTIONr_angle_other_deg0.89435260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58321.875112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41415397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5851529
X-RAY DIFFRACTIONr_chiral_restr0.0590.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02591
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_it1.5747.5561234
X-RAY DIFFRACTIONr_mcbond_other1.5747.551233
X-RAY DIFFRACTIONr_mcangle_it2.88111.3151539
X-RAY DIFFRACTIONr_mcangle_other2.8811.3221540
X-RAY DIFFRACTIONr_scbond_it1.1957.5671174
X-RAY DIFFRACTIONr_scbond_other1.1957.5671167
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.20811.2671689
X-RAY DIFFRACTIONr_long_range_B_refined4.75658.2342584
X-RAY DIFFRACTIONr_long_range_B_other4.75558.2682585
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 50 -
Rwork0.333 1009 -
obs--99.44 %

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