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- PDB-4e2k: The structure of the S. aureus DnaG RNA Polymerase Domain -

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Basic information

Entry
Database: PDB / ID: 4e2k
TitleThe structure of the S. aureus DnaG RNA Polymerase Domain
ComponentsDNA primase
KeywordsTRANSFERASE / Catalytic Domain / Bacterial / apo protein
Function / homology
Function and homology information


DNA primase DnaG / primosome complex / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA helicase activity / DNA-directed RNA polymerase activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
: / DNA primase DnaG, catalytic core, helical bundle / DnaG, RNA polymerase domain, helical bundle / DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / Pheromone ER-1 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Zinc finger, CHC2-type / DNA primase, DnaG ...: / DNA primase DnaG, catalytic core, helical bundle / DnaG, RNA polymerase domain, helical bundle / DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / Pheromone ER-1 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / 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-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / DNA primase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRymer, R.U. / Solorio, F.A. / Clement, C. / Corn, J.E. / Wang, J.D. / Berger, J.M.
CitationJournal: Structure / Year: 2012
Title: Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases.
Authors: Rymer, R.U. / Solorio, F.A. / Tehranchi, A.K. / Chu, C. / Corn, J.E. / Keck, J.L. / Wang, J.D. / Berger, J.M.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9183
Polymers37,6781
Non-polymers2402
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.334, 151.334, 38.571
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DNA primase


Mass: 37677.508 Da / Num. of mol.: 1 / Fragment: UNP residues 111-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dnaG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+
References: UniProt: O05338, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.15M sodium thiocyanate, 0.1M Bis-Tris, 13% PEG3350, 2% Benzamidine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 28064 / Num. obs: 28010 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 30.5
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.15-2.22199
2.22-2.31199
2.31-2.421100
2.42-2.551100
2.55-2.711100
2.71-2.911100
2.91-3.211100
3.21-3.671100
3.67-4.621100
4.62-30.431100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDE

1dde


Resolution: 2.15→30.433 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 1406 5.02 %RANDOM
Rwork0.1908 ---
all0.1921 28064 --
obs0.1921 28010 99.81 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.271 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 32.83 Å2
Baniso -1Baniso -2Baniso -3
1-5.1937 Å20 Å2-0 Å2
2--5.1937 Å20 Å2
3----4.2455 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 18 240 2832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062728
X-RAY DIFFRACTIONf_angle_d0.8043686
X-RAY DIFFRACTIONf_dihedral_angle_d12.2631048
X-RAY DIFFRACTIONf_chiral_restr0.055396
X-RAY DIFFRACTIONf_plane_restr0.004482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.22420.31361250.2432591X-RAY DIFFRACTION99
2.2242-2.31320.29251630.24382610X-RAY DIFFRACTION99
2.3132-2.41840.2211360.22062645X-RAY DIFFRACTION100
2.4184-2.54590.25591410.20452643X-RAY DIFFRACTION100
2.5459-2.70530.24251290.20792659X-RAY DIFFRACTION100
2.7053-2.9140.25321560.20092634X-RAY DIFFRACTION100
2.914-3.2070.23481370.20272663X-RAY DIFFRACTION100
3.207-3.67040.21281460.18562655X-RAY DIFFRACTION100
3.6704-4.62170.19341280.1652715X-RAY DIFFRACTION100
4.6217-30.43630.17271450.17492789X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1173-0.34010.06141.70860.31291.9945-0.02710.05070.0178-0.09330.0024-0.01740.1857-0.29180.24180.4501-0.1976-0.02420.18560.00350.1509-42.2886-55.316-3.5181
20.70360.3246-0.69541.33680.54991.3264-0.03110.0160.0812-0.0453-0.0251-0.1633-0.1591-0.1766-0.00280.412-0.1262-0.04320.1699-0.00150.2251-38.5514-45.46461.7004
33.00652.08720.78444.18561.13491.2325-0.07310.1847-0.0623-0.11630.156-0.46040.18210.10750.00530.322-0.0605-0.070.1683-0.0030.3336-25.337-33.93753.8145
41.3878-0.6087-0.68911.6212-0.46151.1649-0.0067-0.07080.2910.11180.0282-0.2826-0.09960.03-0.0040.2233-0.045-0.05640.1675-0.02190.4174-21.7685-12.11228.4536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 108:211))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 212:252))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 253:362))
4X-RAY DIFFRACTION4chain 'A' and ((resseq 363:428))

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