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- PDB-7ne7: oligopeptidase B from S. proteomaculans with modified hinge regio... -

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Basic information

Entry
Database: PDB / ID: 7ne7
Titleoligopeptidase B from S. proteomaculans with modified hinge region in complex with N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide
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
SPERMINE / Chem-TCK / Oligopeptidase B
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPetrenko, D.E. / Nikolaeva, A.Y. / Lazarenko, V.A. / Dorovatovskiy, P.V. / Vlaskina, A.V. / Mikhailova, A.G. / Rakitina, T.V. / Timofeev, V.I.
CitationJournal: Crystals / Year: 2021
Title: The Crystal Structure of N alpha-p-tosyl-lysyl Chloromethylketone-Bound Oligopeptidase B from Serratia Proteamaculans Revealed a New Type of Inhibitor Binding
Authors: Timofeev, V.I. / Petrenko, D.E. / Agapova, Y.K. / Vlaskina, A.V. / Karlinsky, D.M. / Mikhailova, A.G. / Kuranova, I.P. / Rakitina, T.V.
History
DepositionFeb 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 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)80,3409
Polymers78,4601
Non-polymers1,8808
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint21 kcal/mol
Surface area29420 Å2
Unit cell
Length a, b, c (Å)73.320, 101.100, 108.760
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: 78459.852 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
#2: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H26N4
#3: 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.: 2 / Source method: obtained synthetically / Formula: C14H21ClN2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200 mM Lithium sulfate, 100 mM Bis-Tris pH 5.5, 23% PEG 3350, TCK

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.8 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.3→19.98 Å / Num. obs: 35505 / % possible obs: 99.71 % / Redundancy: 7.92 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.98
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.14 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 2598 / % possible all: 99.01

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TF5

6tf5
PDB Unreleased entry


Resolution: 2.3→19.98 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.571 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1825 5 %RANDOM
Rwork0.1884 ---
obs0.1906 34680 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.56 Å2 / Biso mean: 27.198 Å2 / Biso min: 9.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 124 328 5997
Biso mean--44.59 26.13 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135834
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175327
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.6647898
X-RAY DIFFRACTIONr_angle_other_deg1.2611.59512253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7045682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29822.472356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58415928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0731541
X-RAY DIFFRACTIONr_chiral_restr0.1020.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021430
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 130 -
Rwork0.24 2468 -
all-2598 -
obs--99.01 %

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