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

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Basic information

Entry
Database: PDB / ID: 4edg
TitleThe structure of the S. aureus DnaG RNA Polymerase Domain bound to ATP and Manganese
ComponentsDNA primasePrimase
KeywordsTRANSFERASE / Catalytic Domain / nucleoside triphosphate / nucleoside polyphosphate / protein-ligand complex
Function / homology
Function and homology information


DNA primase DnaG / primosome complex / DNA primase activity / DNA helicase activity / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / ATP binding
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, CHC2-type zinc finger / DNA primase, catalytic core, N-terminal domain superfamily / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / Toprim-like / 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
ADENOSINE-5'-TRIPHOSPHATE / BENZAMIDINE / : / DNA primase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 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 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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)38,5907
Polymers37,6781
Non-polymers9126
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.261, 151.261, 38.665
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 / 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 / Benzamidine


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 63.6 %
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 ATP, 5 mM MnCl2, 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: 2.003→130.996 Å / Num. all: 34568 / Num. obs: 34499 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.046 / Net I/σ(I): 22.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.115.30.2872.82602949150.28798.8
2.11-2.245.50.1784.42606047480.178100
2.24-2.395.50.126.52461244570.12100
2.39-2.595.50.0819.52297641620.081100
2.59-2.835.50.0612.52082438140.06100
2.83-3.175.50.04316.81909834740.043100
3.17-3.665.40.03319.91678830810.03399.9
3.66-4.485.30.03120.11398526280.03199.9
4.48-6.335.20.02722.31075020540.02799.9
6.33-43.6655.10.02325597111660.02398.9

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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
Starting model: pdb entry 4E2K

4e2k


Resolution: 2.003→43.665 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 1705 4.94 %copied from 4E2K
Rwork0.1615 ---
obs0.1633 34480 99.74 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.329 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 101.77 Å2 / Biso mean: 34.795 Å2 / Biso min: 14.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.6171 Å2-0 Å2-0 Å2
2--2.6171 Å20 Å2
3----5.2342 Å2
Refinement stepCycle: LAST / Resolution: 2.003→43.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 52 350 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082769
X-RAY DIFFRACTIONf_angle_d1.0623757
X-RAY DIFFRACTIONf_chiral_restr0.066402
X-RAY DIFFRACTIONf_plane_restr0.004481
X-RAY DIFFRACTIONf_dihedral_angle_d13.8091052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0029-2.06180.26581180.21142665278398
2.0618-2.12830.21051390.180127052844100
2.1283-2.20440.22531350.172327092844100
2.2044-2.29270.22071510.162627252876100
2.2927-2.3970.20181510.159627112862100
2.397-2.52340.20661450.161626872832100
2.5234-2.68140.19411320.167227342866100
2.6814-2.88840.20831670.162427152882100
2.8884-3.1790.21251370.17127572894100
3.179-3.63890.2051520.168327232875100
3.6389-4.58380.16811300.140927872917100
4.5838-43.67560.17521480.15612857300599
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)
11.1963-0.4759-0.35130.9999-0.29812.38650.01870.0499-0.0124-0.00410.00210.03540.1956-0.06380.01340.24560.1331-0.01350.1576-0.01570.108225.7354-63.2181-7.8824
21.2436-0.6434-0.34933.05220.22520.5082-0.0427-0.10010.15160.0479-0.0044-0.00610.07130.08-0.01430.19250.1049-0.03680.1737-0.06290.17716.0761-42.9051.6297
30.18240.03-0.01230.1167-0.08490.09780.06090.35060.2671-0.51070.0641-0.2729-0.47260.4190.00010.54270.03230.1010.3457-0.04680.416922.2235-32.3238-11.2401
41.87980.15670.20621.4876-0.5520.82250.0177-0.18960.24870.10320.03330.1156-0.0177-0.0569-0.00060.1950.0386-0.01020.1594-0.04870.3283-0.6938-25.27723.7241
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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