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- PDB-5w34: Crystal structure of the RNA polymerase domain (RPD) of Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 5w34
TitleCrystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with double-stranded DNA GACCGGAAGTGG
Components
  • DNA oligomer 5'-CCACTTCCGGTC
  • DNA oligomer 5'-GACCGGAAGTGG
  • DNA primase
KeywordsTRANSFERASE / 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
DNA / DNA (> 10) / DNA primase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHou, C. / 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
B: DNA primase
C: DNA oligomer 5'-CCACTTCCGGTC
D: DNA oligomer 5'-GACCGGAAGTGG


Theoretical massNumber of molelcules
Total (without water)78,2284
Polymers78,2284
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-14 kcal/mol
Surface area33010 Å2
Unit cell
Length a, b, c (Å)43.781, 212.116, 47.418
Angle α, β, γ (deg.)90.00, 107.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA primase


Mass: 35450.410 Da / Num. of mol.: 2
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: DNA chain DNA oligomer 5'-CCACTTCCGGTC


Mass: 3574.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA oligomer 5'-GACCGGAAGTGG


Mass: 3752.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 100 mM Hepes pH 7.0, 7% w/v PEG 4000

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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: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 16383 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Net I/σ(I): 21

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W33

5w33


Resolution: 2.95→35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / SU B: 25.535 / SU ML: 0.452 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28532 781 4.8 %RANDOM
Rwork0.23578 ---
obs0.23829 15508 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.86 Å20 Å2-1.46 Å2
2---4.12 Å20 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 2.95→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 252 0 0 5137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195259
X-RAY DIFFRACTIONr_bond_other_d0.0020.024819
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9077131
X-RAY DIFFRACTIONr_angle_other_deg0.944311063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55222.085235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39915816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2241558
X-RAY DIFFRACTIONr_chiral_restr0.060.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021221
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_it2.758.9622549
X-RAY DIFFRACTIONr_mcbond_other2.7518.9612548
X-RAY DIFFRACTIONr_mcangle_it4.77613.4373181
X-RAY DIFFRACTIONr_mcangle_other4.77613.4383182
X-RAY DIFFRACTIONr_scbond_it2.33510.0452710
X-RAY DIFFRACTIONr_scbond_other2.33610.0432709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1715.0013951
X-RAY DIFFRACTIONr_long_range_B_refined7.215768
X-RAY DIFFRACTIONr_long_range_B_other7.215769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 58 -
Rwork0.296 1086 -
obs--94.47 %

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