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- PDB-4c2g: Crystal structure of CtpB(S309A) in complex with a peptide having... -

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Basic information

Entry
Database: PDB / ID: 4c2g
TitleCrystal structure of CtpB(S309A) in complex with a peptide having a Val-Pro-Ala C-terminus
Components
  • (CARBOXY-TERMINAL PROCESSING PROTEASE CTPB) x 2
  • PEPTIDE1
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / PDZ-PROTEASES / ALLOSTERIC REGULATION / CONFORMATIONAL SWITCH / SPORULATION / 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
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 ...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)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1Jan 8, 2014Group: Source and taxonomy
Revision 1.2Jul 15, 2015Group: Data collection
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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

Downloads & links

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Assembly

Deposited unit
A: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
B: PEPTIDE1
C: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB


Theoretical massNumber of molelcules
Total (without water)51,2853
Polymers51,2853
Non-polymers00
Water6,467359
1
A: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
B: PEPTIDE1
C: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB

A: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
B: PEPTIDE1
C: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB


Theoretical massNumber of molelcules
Total (without water)102,5706
Polymers102,5706
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area7730 Å2
ΔGint-49 kcal/mol
Surface area41830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.712, 118.712, 72.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2139-

HOH

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Components

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


Mass: 49724.480 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-478 / 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: Protein/peptide PEPTIDE1


Mass: 302.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PEPTIDE CO-PURIFIED FROM E. COLI EXPRESSION / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21
#3: Protein/peptide CARBOXY-TERMINAL PROCESSING PROTEASE CTPB / PEPTIDE VPA / CTPB / C-TERMINAL PROCESSING PROTEASE


Mass: 1258.419 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-40 / Source method: obtained synthetically / Details: PEPTIDE NH2-EMDKPQTAAVPA-COOH
Source: (synth.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
References: UniProt: O35002, C-terminal processing peptidase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.87 Å3/Da / Density % sol: 57.14 % / Description: NONE
Crystal growDetails: 2.1 M NA-MALONATE PH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→102.81 Å / Num. obs: 45714 / % possible obs: 98.5 % / Observed criterion σ(I): -10 / Redundancy: 3.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / % possible all: 97.5

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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: 1.9→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 2269 4.9 %RANDOM
Rwork0.2035 ---
obs0.2035 45467 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.385 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.578 Å20 Å20 Å2
2--4.578 Å20 Å2
3----9.156 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 0 359 3786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.31
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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