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- PDB-4c2e: Crystal structure of the protease CtpB(S309A) present in a restin... -

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Basic information

Entry
Database: PDB / ID: 4c2e
TitleCrystal structure of the protease CtpB(S309A) present in a resting state
ComponentsCARBOXY-TERMINAL PROCESSING PROTEASE CTPB
KeywordsHYDROLASE / PROTEOLYTIC TUNNEL
Function / homology
Function and homology information


C-terminal processing peptidase / peptide metabolic process / sporulation resulting in formation of a cellular spore / peptide binding / peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / serine-type endopeptidase activity / signal transduction / protein homodimerization activity ...C-terminal processing peptidase / peptide metabolic process / sporulation resulting in formation of a cellular spore / peptide binding / peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / serine-type endopeptidase activity / signal transduction / protein homodimerization activity / proteolysis / identical protein binding
Similarity search - Function
Activating protease CtpB N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / PGBD superfamily / PDZ domain / PDZ domain / Peptidoglycan binding-like / Putative peptidoglycan binding domain ...Activating protease CtpB N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / PGBD superfamily / PDZ domain / PDZ domain / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / ClpP/crotonase-like domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Carboxy-terminal processing protease CtpB
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMastny, M. / Heuck, A. / Kurzbauer, R. / Clausen, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Ctpb Assembles a Gated Protease Tunnel Regulating Cell-Cell Signaling During Spore Formation in Bacillus Subtilis.
Authors: Mastny, M. / Heuck, A. / Kurzbauer, R. / Heiduk, A. / Boisguerin, P. / Volkmer, R. / Ehrmann, M. / Rodrigues, C.D.A. / Rudner, D.Z. / Clausen, T.
History
DepositionAug 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

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Assembly

Deposited unit
A: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
B: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB


Theoretical massNumber of molelcules
Total (without water)99,5372
Polymers99,5372
Non-polymers00
Water17,745985
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-31 kcal/mol
Surface area39820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.052, 72.687, 79.569
Angle α, β, γ (deg.)117.09, 90.45, 102.71
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CARBOXY-TERMINAL PROCESSING PROTEASE CTPB / C-TERMINAL PROCESSING PROTEASE / CTPB


Mass: 49768.535 Da / Num. of mol.: 2 / Fragment: RESIDUES 44-480 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: O35002, C-terminal processing peptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2.71 Å3/Da / Density % sol: 54.55 % / Description: NONE
Crystal growDetails: 10% ISOPROPANOL, 0.1 M IMIDAZOL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→46.28 Å / Num. obs: 93531 / % possible obs: 96.7 % / Observed criterion σ(I): -10 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.6 / % possible all: 95.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C2C

4c2c


Resolution: 1.8→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 4708 4.9 %RANDOM
Rwork0.1824 ---
obs0.1824 93488 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.5397 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.865 Å23.329 Å2-0.675 Å2
2--5.782 Å20.471 Å2
3---0.083 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6794 0 0 985 7779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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