[English] 日本語
Yorodumi
- PDB-4tps: Sporulation Inhibitor of DNA Replication, SirA, in complex with D... -

+
Open data


ID or keywords:

Loading...

-
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


DnaA-oriC complex / sporulation resulting in formation of a cellular spore / negative regulation of DNA replication / nucleoid / regulation of DNA replication / DNA replication origin binding / DNA replication initiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity ...DnaA-oriC complex / sporulation resulting in formation of a cellular spore / negative regulation of DNA replication / nucleoid / regulation of DNA replication / DNA replication origin binding / DNA replication initiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity / lipid binding / DNA-templated transcription / 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, conserved site / DnaA protein signature. ...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, conserved site / DnaA protein signature. / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Bacterial dnaA protein helix-turn-helix / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / 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 / Chromosomal replication initiator protein DnaA / Sporulation inhibitor of replication protein SirA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (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
Revision 2.0Sep 23, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)57,1475
Polymers57,0884
Non-polymers591
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)28,6033
Polymers28,5442
Non-polymers591
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


Theoretical massNumber of molelcules
Total (without water)28,5442
Polymers28,5442
Non-polymers00
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 (eV)
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

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

-
Components

#1: Protein Sporulation inhibitor of replication protein SirA


Mass: 18799.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: sirA, orf148, pcfA, 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 subsp. subtilis str. 168 (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-ACT / ACETATE ION


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more