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- PDB-2alj: Structure of the cis confomer of the major extracytoplasmic domai... -

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Basic information

Entry
Database: PDB / ID: 2alj
TitleStructure of the cis confomer of the major extracytoplasmic domain of the bacterial cell division protein divib from geobacillus stearothermophilus
Componentscell-division initiation protein
KeywordsCELL CYCLE / CELL-DIVISION INITIATION PROTEIN / DIVIB / FTSQ / DIVISOME
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / cell division site / plasma membrane
Similarity search - Function
Rossmann fold - #10960 / Cell division protein DivIB / : / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / POTRA domain / POTRA domain profile. / Rossmann fold ...Rossmann fold - #10960 / Cell division protein DivIB / : / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / POTRA domain / POTRA domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein DivIB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS (CANDID, CYANA), SIMULATED ANNEALING (XPLOR)
AuthorsRobson, S.A. / King, G.F.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Domain architecture and structure of the bacterial cell division protein DivIB
Authors: Robson, S.A. / King, G.F.
#1: Journal: J.BACTERIOL. / Year: 1989
Title: Cloning and expression of a bacillus subtilis division initiation gene for which a homolog has not been identified in another organism
Authors: Harry, E.J. / Wake, R.G.
#2: Journal: J.BACTERIOL. / Year: 1989
Title: Nucleotide sequence and insertional inactivation of a bacillus subtilis gene that affects cell division, sporulation, and temperature sensitivity
Authors: Beall, B. / Lutkenhaus, J.
#3: Journal: MOL.MICROBIOL. / Year: 1997
Title: DIVIB, FTSZ and cell division in bacillus subtilis
Authors: Rowland, S.L. / Katis, V.L. / Partridge, S.R. / Wake, R.G.
#4: Journal: J.BACTERIOL. / Year: 1999
Title: Membrane-bound division proteins DivIB and DivIC of bacillus subtilis function solely through their external domains in both vegetative and sporulation division
Authors: Katis, V.L. / Wake, R.G.
History
DepositionAug 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 999SEQUENCE DIVIB FRAGMENT WAS SUBCLONED AS A TRANSLATIONAL FUSION TO THE C-TERMINUS OF SCHISTOSOMA ...SEQUENCE DIVIB FRAGMENT WAS SUBCLONED AS A TRANSLATIONAL FUSION TO THE C-TERMINUS OF SCHISTOSOMA JAPONICUM GLUTATHIONE S-TRANSFERASE. THE GENE SEQUENCE ENCODING THIS PROTEIN DOMAIN WAS CLONED USING CHROMOSOMAL DNA FROM GEOBACILLUS STEAROTHERMOPHILUS. The sequence matches that of THE CORRESPONDING DOMAIN OF the DIVIB ORTHOLOG from Geobacillus kaustophilus (SWISS-PROT ENTRY Q5L0X5_GEOKA and Genbank GI:56419655).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cell-division initiation protein


Theoretical massNumber of molelcules
Total (without water)13,3651
Polymers13,3651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 60STRUCTURES WITH LOWEST ENERGY AND NO RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein cell-division initiation protein / DivIB / FTSQ


Mass: 13365.084 Da / Num. of mol.: 1 / Fragment: beta domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DivIB / Plasmid: PSAR19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5L0X5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
131HNHA
141HNHB

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Sample preparation

DetailsContents: 1 MM DIVIB, 150 MM NACL, 10 MM SODIUM PHOSPHATE, 10 MICROMOLAR EDTA, 10 MICROMOLAR 4-(2- AMINOETHYL)BENZENESULFONYL FLOURIDE (AEBSF), 0.02% SODIUM AZIDE, PH 6.0, 92.5% H2O, 7.5% D2O; 1 MM ...Contents: 1 MM DIVIB, 150 MM NACL, 10 MM SODIUM PHOSPHATE, 10 MICROMOLAR EDTA, 10 MICROMOLAR 4-(2- AMINOETHYL)BENZENESULFONYL FLOURIDE (AEBSF), 0.02% SODIUM AZIDE, PH 6.0, 92.5% H2O, 7.5% D2O; 1 MM DIVIB, 150 MM NACL, 10 MM SODIUM PHOSPHATE, 10 MICROMOLAR EDTA, 10 MICROMOLAR 4- (2-AMINOETHYL)BENZENESULFONYL FLOURIDE (AEBSF), 0.02% SODIUM AZIDE, PH 6.0, 100% D2O
Sample conditionsIonic strength: 0.16 / pH: 6 / Pressure: AMBIENT / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1AXEL T. BRUNGERrefinement
NMRPipe2.2structure solution
XEASY1.3.13structure solution
Cstructure solution
ID/CYANA1.1structure solution
RefinementMethod: TORSION ANGLE DYNAMICS (CANDID, CYANA), SIMULATED ANNEALING (XPLOR)
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2544 NOE-DERIVED DISTANCE RESTRAINTS, 88 RESTRAINTS DEFINING 44 HYDROGEN BONDS, AND 197 DIHEDRAL ANGLE RESTRAINTS
NMR ensembleConformer selection criteria: STRUCTURES WITH LOWEST ENERGY AND NO RESTRAINT VIOLATIONS
Conformers calculated total number: 60 / Conformers submitted total number: 25

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