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

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Basic information

Entry
Database: PDB / ID: 4edr
TitleThe structure of the S. aureus DnaG RNA Polymerase Domain bound to UTP and Manganese
ComponentsDNA primase
KeywordsTRANSFERASE / Catalytic Domain / nucleoside triphosphate / nucleoside polyphosphate / protein-ligand 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 / : / URIDINE 5'-TRIPHOSPHATE / DNA primase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHENIX Automolecular replacement / Resolution: 2.01 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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)38,6878
Polymers37,6781
Non-polymers1,0097
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.582, 150.582, 38.633
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.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*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


Mass: 18.015 Da / Num. of mol.: 377 / 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: 3.35 Å3/Da / Density % sol: 63.24 %
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 UTP, 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: 2.01→38.63 Å / Num. all: 33898 / Num. obs: 33865 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 23.42 Å2 / Rsym value: 0.047 / Net I/σ(I): 22.6
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.01-2.125.43.60.1731100
2.12-2.255.56.30.1191100
2.25-2.45.580.0841100
2.4-2.595.511.80.0631100
2.59-2.845.511.80.0511100
2.84-3.185.514.60.0441100
3.18-3.675.312.30.0471100
3.67-4.495.315.70.0381100
4.49-6.365.321.80.0251100
6.36-38.635.129.90.02198.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: PHENIX Automolecular replacement
Resolution: 2.01→37.042 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.12 / σ(F): 0 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 1713 5.06 %
Rwork0.1716 --
obs0.1733 33847 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.942 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 78.34 Å2 / Biso mean: 28.8111 Å2 / Biso min: 12.93 Å2
Baniso -1Baniso -2Baniso -3
1-2.5316 Å2-0 Å2-0 Å2
2--2.5316 Å20 Å2
3----5.0632 Å2
Refinement stepCycle: LAST / Resolution: 2.01→37.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 59 377 3018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022703
X-RAY DIFFRACTIONf_angle_d0.7183648
X-RAY DIFFRACTIONf_chiral_restr0.047392
X-RAY DIFFRACTIONf_plane_restr0.003471
X-RAY DIFFRACTIONf_dihedral_angle_d12.8451017
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 (%)
2.01-2.06920.22121430.179626182761100
2.0692-2.13590.20481500.173826812831100
2.1359-2.21230.23751280.17426402768100
2.2123-2.30080.21781590.164426232782100
2.3008-2.40550.18071440.176326822826100
2.4055-2.53230.19751390.17426572796100
2.5323-2.69090.22131270.174126902817100
2.6909-2.89860.22031630.183626392802100
2.8986-3.19020.23661390.18127042843100
3.1902-3.65150.21421460.169326712817100
3.6515-4.59910.17881300.152227392869100
4.5991-37.0480.18831450.17822790293599
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)
10.7455-0.45-0.14140.795-0.18932.08970.02040.0274-0.0332-0.0273-0.01610.02280.1832-0.0468-0.00390.19330.0928-0.01230.121-0.01430.087125.6995-62.6804-3.6664
20.9781-0.4567-0.27382.32350.21950.5755-0.0343-0.1130.16710.17460.01250.0443-0.0086-0.0084-0.02650.15390.1309-0.03220.1068-0.0510.144716.4141-42.62436.1443
30.19920.04140.05970.2580.10560.59510.04650.23090.232-0.6264-0.0836-0.0703-0.70870.2088-0.00390.37930.04610.04130.2627-0.00330.333722.3661-32.3372-6.8339
41.4490.14440.11171.2927-0.6230.71280.0216-0.210.27780.16680.03280.1135-0.0012-0.1047-0.00180.19170.0364-0.00240.1496-0.05890.3193-0.2348-24.97888.2577
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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