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

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Basic information

Entry
Database: PDB / ID: 4edv
TitleThe structure of the S. aureus DnaG RNA Polymerase Domain bound to pppGpp 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
Chem-0O2 / BENZAMIDINE / : / DNA primase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR 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 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Feb 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)38,6466
Polymers37,6781
Non-polymers9685
Water5,386299
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, 38.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N5O20P5
#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.: 299 / 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: 63.66 %
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 pppGpp, 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: 2.01→131.059 Å / Num. obs: 34211 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 31.06 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.8
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4959 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→37.108 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.26 / σ(F): 1.46 / Phase error: 18.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 1739 5.09 %copied from 4E2K
Rwork0.1668 ---
obs0.1686 34198 99.78 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.177 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 156.1 Å2 / Biso mean: 39.3728 Å2 / Biso min: 18.69 Å2
Baniso -1Baniso -2Baniso -3
1-3.547 Å20 Å2-0 Å2
2--3.547 Å20 Å2
3----7.0941 Å2
Refinement stepCycle: LAST / Resolution: 2.01→37.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 52 299 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032720
X-RAY DIFFRACTIONf_angle_d0.723679
X-RAY DIFFRACTIONf_chiral_restr0.052394
X-RAY DIFFRACTIONf_plane_restr0.003471
X-RAY DIFFRACTIONf_dihedral_angle_d13.7441040
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 (%)
2.01-2.06920.32221450.239526592804100
2.0692-2.1360.2211640.19926922856100
2.136-2.21230.24121250.182526602785100
2.2123-2.30090.20931560.166826882844100
2.3009-2.40560.19461540.169326882842100
2.4056-2.53240.19931380.161626672805100
2.5324-2.6910.22871310.174527132844100
2.691-2.89870.22351640.171426702834100
2.8987-3.19020.22041370.173127342871100
3.1902-3.65150.20411470.166727032850100
3.6515-4.59920.16351340.140527702904100
4.5992-37.11430.18821440.16762815295999
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)
11.92170.0277-0.06460.5399-0.29832.2019-0.01910.0671-0.0711-0.03160.0306-0.02150.16890.18750.0150.1039-0.0308-0.00040.4708-0.01510.1524143.2749121.5898-3.3855
23.5189-0.6506-0.35271.3488-0.16780.71430.0034-0.1080.01550.07280.01810.1369-0.01320.1243-0.00520.0825-0.03360.03390.3403-0.03540.2072121.0324123.71666.2889
30.28630.13460.12490.34920.0340.69390.03290.61010.1014-0.4369-0.21050.1194-0.6959-0.3069-0.01190.34180.04630.06330.58640.08040.433115.0045134.2569-6.6382
41.64810.64750.5192.3593-0.12071.11250.062-0.15530.00080.0802-0.05170.13460.0312-0.0667-0.00030.15620.01910.05040.2484-0.00850.381797.2101118.02148.6388
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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