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- PDB-4tps: Sporulation Inhibitor of DNA Replication, SirA, in complex with D... -

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Basic information

Entry
Database: PDB / ID: 4tps
TitleSporulation Inhibitor of DNA Replication, SirA, in complex with Domain I of DnaA
Components
  • Chromosomal replication initiator protein DnaA
  • Sporulation inhibitor of replication protein SirA
KeywordsREPLICATION / Sporulation / Inhibitory complex
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / negative regulation of DNA replication / DNA replication origin binding / regulation of DNA replication / DNA replication initiation / DNA replication / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Sporulation inhibitor of replication protein SirA / Sporulation inhibitor of replication protein SirA / SirA superfamily / Sporulation inhibitor of replication protein SirA / DnaA, N-terminal domain / DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal ...Sporulation inhibitor of replication protein SirA / Sporulation inhibitor of replication protein SirA / SirA superfamily / Sporulation inhibitor of replication protein SirA / DnaA, N-terminal domain / DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial dnaA protein / Trp repressor/replication initiator / TATA-Binding Protein / GMP Synthetase; Chain A, domain 3 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / Chromosomal replication initiator protein DnaA / Sporulation inhibitor of replication protein SirA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsJameson, K.H. / Turkenburg, J.P. / Fogg, M.J. / Grahl, A. / Wilkinson, A.J.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structure and interactions of the Bacillus subtilis sporulation inhibitor of DNA replication, SirA, with domain I of DnaA.
Authors: Jameson, K.H. / Rostami, N. / Fogg, M.J. / Turkenburg, J.P. / Grahl, A. / Murray, H. / Wilkinson, A.J.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Apr 3, 2024Group: 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sporulation inhibitor of replication protein SirA
B: Chromosomal replication initiator protein DnaA
C: Sporulation inhibitor of replication protein SirA
D: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1517
Polymers56,9354
Non-polymers2153
Water5,314295
1
A: Sporulation inhibitor of replication protein SirA
B: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6054
Polymers28,4682
Non-polymers1372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-11 kcal/mol
Surface area12510 Å2
MethodPISA
2
C: Sporulation inhibitor of replication protein SirA
D: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5463
Polymers28,4682
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.287, 34.685, 84.735
Angle α, β, γ (deg.)90.00, 102.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROAA2 - 1418 - 147
21GLUGLUPROPROCC2 - 1418 - 147
12ALAALAILEILEBB0 - 803 - 83
22ALAALAILEILEDD0 - 803 - 83

NCS ensembles :
ID
1
2

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Components

#1: Protein Sporulation inhibitor of replication protein SirA / SirA


Mass: 18723.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: sirA, yneE, yoxF, BSU17900 / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45707
#2: Protein Chromosomal replication initiator protein DnaA / Domain I of DnaA


Mass: 9744.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: dnaA, dnaH, BSU00010 / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05648
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.5, 200 mM NH4 acetate, 25 % (w/v) PEG 3350, 1% (v/v) DMF
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→82.86 Å / Num. obs: 52893 / % possible obs: 98.9 % / Redundancy: 2.8 % / Net I/σ(I): 12.5

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementResolution: 1.65→82.86 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.737 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19293 2707 5.1 %RANDOM
Rwork0.12638 ---
obs0.12968 50178 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20.47 Å2
2---0.59 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.65→82.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 12 295 4066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193907
X-RAY DIFFRACTIONr_bond_other_d0.0010.023680
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9455280
X-RAY DIFFRACTIONr_angle_other_deg0.84638484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7415452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64224.091198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67115712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7721518
X-RAY DIFFRACTIONr_chiral_restr0.1080.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0842.2911794
X-RAY DIFFRACTIONr_mcbond_other4.0762.2891792
X-RAY DIFFRACTIONr_mcangle_it4.7823.442238
X-RAY DIFFRACTIONr_mcangle_other4.7853.4422239
X-RAY DIFFRACTIONr_scbond_it6.3132.9212113
X-RAY DIFFRACTIONr_scbond_other6.3122.922114
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9124.1343039
X-RAY DIFFRACTIONr_long_range_B_refined6.61120.4014622
X-RAY DIFFRACTIONr_long_range_B_other6.44819.9384505
X-RAY DIFFRACTIONr_rigid_bond_restr4.96837587
X-RAY DIFFRACTIONr_sphericity_free29.918595
X-RAY DIFFRACTIONr_sphericity_bonded15.54957682
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43430.16
12C43430.16
21B25160.11
22D25160.11
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 214 -
Rwork0.179 3679 -
obs--99.08 %

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