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- PDB-7ywp: Closed conformation of Oligopeptidase B from Serratia proteomacul... -

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Basic information

Entry
Database: PDB / ID: 7ywp
TitleClosed conformation of Oligopeptidase B from Serratia proteomaculans with covalently bound TCK
ComponentsOligopeptidase B
KeywordsHYDROLASE
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
: / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-TCK / Oligopeptidase B
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPetrenko, D.E. / Boyko, K.M. / Nikolaeva, A.Y. / Vlaskina, A.V. / Mikhailova, A.G. / Timofeev, V.I. / Rakitina, T.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2023
Title: Crystal Structure of Inhibitor-Bound Bacterial Oligopeptidase B in the Closed State: Similarity and Difference between Protozoan and Bacterial Enzymes.
Authors: Petrenko, D.E. / Karlinsky, D.M. / Gordeeva, V.D. / Arapidi, G.P. / Britikova, E.V. / Britikov, V.V. / Nikolaeva, A.Y. / Boyko, K.M. / Timofeev, V.I. / Kuranova, I.P. / Mikhailova, A.G. / ...Authors: Petrenko, D.E. / Karlinsky, D.M. / Gordeeva, V.D. / Arapidi, G.P. / Britikova, E.V. / Britikov, V.V. / Nikolaeva, A.Y. / Boyko, K.M. / Timofeev, V.I. / Kuranova, I.P. / Mikhailova, A.G. / Bocharov, E.V. / Rakitina, T.V.
History
DepositionFeb 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligopeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5932
Polymers78,2611
Non-polymers3331
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint2 kcal/mol
Surface area26920 Å2
Unit cell
Length a, b, c (Å)75.529, 89.660, 108.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oligopeptidase B


Mass: 78260.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (bacteria) / Gene: opdB / Production host: Escherichia coli (E. coli) / References: UniProt: B3VI58, EC: 3.4.21.83
#2: Chemical ChemComp-TCK / N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide / Tos-Lys-CH2Cl


Type: peptide-like / Mass: 332.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21ClN2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200 mM Lithium sulfate, 100 mM Bis-Tris pH 5.5, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 37524 / % possible obs: 98.57 % / Redundancy: 4.14 % / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.09 / Net I/σ(I): 6.6952
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.27 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.89 / Num. unique obs: 5487 / Rrim(I) all: 0.27 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OB1

7ob1


Resolution: 2.2→29.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.226 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 1877 5 %RANDOM
Rwork0.1845 ---
obs0.1879 35605 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.24 Å2 / Biso mean: 22.959 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.2→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 20 417 5968
Biso mean--24.42 26.95 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135697
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155125
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6567744
X-RAY DIFFRACTIONr_angle_other_deg1.2571.58511790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8075675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70322.422351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74715922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6111541
X-RAY DIFFRACTIONr_chiral_restr0.070.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021404
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 148 -
Rwork0.204 2610 -
all-2758 -
obs--99.71 %

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