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- PDB-1dz3: DOMAIN-SWAPPING IN THE SPORULATION RESPONSE REGULATOR SPO0A -

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Basic information

Entry
Database: PDB / ID: 1dz3
TitleDOMAIN-SWAPPING IN THE SPORULATION RESPONSE REGULATOR SPO0A
ComponentsStage 0 sporulation protein A
KeywordsRESPONSE REGULATOR / DOMAIN SWAPPING
Function / homology
Function and homology information


detection of stimulus / regulation of sporulation resulting in formation of a cellular spore / phosphorelay response regulator activity / sporulation resulting in formation of a cellular spore / DNA-binding transcription factor activity / calcium ion binding / DNA binding / cytoplasm
Similarity search - Function
Sporulation transcription factor Spo0A / Sporulation initiation factor Spo0A, C-terminal / Sporulation initiation factor Spo0A C terminal / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator ...Sporulation transcription factor Spo0A / Sporulation initiation factor Spo0A, C-terminal / Sporulation initiation factor Spo0A C terminal / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Stage 0 sporulation protein A
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsLewis, R.J. / Brannigan, J.A. / Muchova, K. / Leonard, G. / Barak, I. / Wilkinson, A.J.
CitationJournal: J. Mol. Biol. / Year: 2000
Title: Domain swapping in the sporulation response regulator Spo0A.
Authors: Lewis, R.J. / Muchova, K. / Brannigan, J.A. / Barak, I. / Leonard, G. / Wilkinson, A.J.
History
DepositionFeb 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stage 0 sporulation protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8412
Polymers14,7451
Non-polymers961
Water1,71195
1
A: Stage 0 sporulation protein A
hetero molecules

A: Stage 0 sporulation protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6824
Polymers29,4902
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4000 Å2
ΔGint-39.8 kcal/mol
Surface area15560 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.024, 59.024, 66.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsBIOMOLECULEDIMER CRYSTALLISED AROUND CRYSTALLOGRAPHIC TWO-FOLDBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein Stage 0 sporulation protein A


Mass: 14745.070 Da / Num. of mol.: 1 / Fragment: RECEIVER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cellular location: CYTOPLASM / Gene: spo0A / Plasmid: PET / Cellular location (production host): CYTOPLASM / Gene (production host): SPO0A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P52934
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL DOMAIN ONLY, RESIDUES 1 - 130

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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: 2.7 Å3/Da / Density % sol: 50 %
Crystal growpH: 4
Details: 10 % PEG 4000, 100 MM LITHIUM SULPHATE 100 MM SODIUM ACETATE, PH 4.0
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
210 mMdithiothreitol1drop
3100 mMsodium acetate1reservoir
410 %(w/v)PEG40001reservoir
5100 mMlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.65→28 Å / Num. obs: 16570 / % possible obs: 99.4 % / Redundancy: 8.7 % / Biso Wilson estimate: 29.133 Å2 / Rsym value: 0.056 / Net I/σ(I): 24.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.268 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 143244 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.268

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→28 Å / SU B: 2.04504 / SU ML: 0.07071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.10422 / ESU R Free: 0.11453
RfactorNum. reflection% reflectionSelection details
Rfree0.26593 843 5 %RANDOM
Rwork0.20774 ---
obs0.23538 15811 99.4 %-
Displacement parametersBiso mean: 34.031 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 5 95 1074
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.663
X-RAY DIFFRACTIONp_mcangle_it3.8125
X-RAY DIFFRACTIONp_scbond_it4.3956
X-RAY DIFFRACTIONp_scangle_it5.6078
X-RAY DIFFRACTIONp_plane_restr0.02420.03
X-RAY DIFFRACTIONp_chiral_restr0.1270.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd00.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.0980.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor14.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor16.720
X-RAY DIFFRACTIONp_special_tor015

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