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- PDB-4edt: The structure of the S. aureus DnaG RNA Polymerase Domain bound t... -

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Basic information

Entry
Database: PDB / ID: 4edt
TitleThe structure of the S. aureus DnaG RNA Polymerase Domain bound to ppGpp and Manganese
ComponentsDNA primase
Keywordstransferase/transferase inhibitor / Catalytic Domain / Bacterial / nucleotide / nucleoside triphosphate / nucleoside polyphosphate / protein-ligand complex / transferase / transferase-transferase inhibitor complex
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 / GUANOSINE-5',3'-TETRAPHOSPHATE / : / DNA primase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsRymer, R.U. / Solorio, F.A. / Chu, 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 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)38,5115
Polymers37,6781
Non-polymers8334
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.164, 152.164, 38.769
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Detailsmonomer

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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 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+
References: UniProt: O05338, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3.43 Å3/Da / Density % sol: 64.12 %
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, 2.5 mM ppGpp, 10 mM MnCl2, 1 mM MgCl2, 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 315r / 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: 2.005→131.405 Å / Num. all: 34635 / Num. obs: 34635 / % possible obs: 99.7 % / Redundancy: 8.2 % / Rsym value: 0.075
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.63 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.005→43.926 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.22 / σ(F): 1.35 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1765 5.04 %copied from 4E2K
Rwork0.1797 ---
obs0.182 34635 99.73 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.086 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 148.06 Å2 / Biso mean: 36.3554 Å2 / Biso min: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.3141 Å20 Å2-0 Å2
2--2.3141 Å20 Å2
3----4.6283 Å2
Refinement stepCycle: LAST / Resolution: 2.005→43.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 47 338 2963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042716
X-RAY DIFFRACTIONf_angle_d0.8283678
X-RAY DIFFRACTIONf_chiral_restr0.057397
X-RAY DIFFRACTIONf_plane_restr0.004473
X-RAY DIFFRACTIONf_dihedral_angle_d12.9371031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0029-2.05710.25531260.21972491261797
2.0571-2.11760.24321330.192425122645100
2.1176-2.18590.23711520.196725242676100
2.1859-2.26410.36741190.284125452664100
2.2641-2.35470.25071510.240225182669100
2.3547-2.46190.21981440.174425412685100
2.4619-2.59170.24071270.170125732700100
2.5917-2.7540.20971360.17325452681100
2.754-2.96660.2151440.170325422686100
2.9666-3.26510.23271310.172825572688100
3.2651-3.73730.24211420.189425772719100
3.7373-4.70770.19141180.14326162734100
4.7077-43.93650.20071420.172926822824100
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)
11.02410.316-0.40690.80930.05492.22630.0075-0.0389-0.00840.0203-0.0142-0.02930.23220.05220.0160.2456-0.1251-0.00920.13640.02220.081350.004668.58081.0703
21.35180.8161-0.313.3578-0.31650.53960.01190.07670.161-0.04620.0026-0.00980.1183-0.10660.0010.1498-0.0896-0.00320.11140.03540.15259.481888.8374-8.5625
30.17440.01960.0080.11160.1020.09370.0678-0.33010.16630.73770.20170.4498-0.4142-0.38080.00020.50870.00550.19260.3160.06990.386553.260199.35284.4037
41.4906-0.21210.23581.17840.35690.8316-0.04580.18410.206-0.03960.0339-0.147-0.03920.1089-0.00390.1759-0.03390.01120.13110.06270.34576.312106.5313-10.7862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 108:233)A108 - 233
2X-RAY DIFFRACTION2chain 'A' and (resseq 234:343)A234 - 343
3X-RAY DIFFRACTION3chain 'A' and (resseq 344:362)A344 - 362
4X-RAY DIFFRACTION4chain 'A' and (resseq 363:428)A363 - 428

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