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- PDB-7ob1: OLIGOPEPTIDASE B FROM S. PROTEOMACULANS WITH MODIFIED HINGE -

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Basic information

Entry
Database: PDB / ID: 7ob1
TitleOLIGOPEPTIDASE B FROM S. PROTEOMACULANS WITH MODIFIED HINGE
ComponentsOligopeptidase B
KeywordsHYDROLASE / PEPTIDASE
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 / Oligopeptidase B
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPetrenko, D.E. / Nikolaeva, A.Y. / Lazarenko, V.A. / Dorovatovskiy, P.V. / Vlaskina, A.V. / Korzhenevskiy, D.A. / Mikhailova, A.G. / Rakitina, T.V. / Timofeev, V.I.
CitationJournal: Biology (Basel) / Year: 2021
Title: First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine.
Authors: Petrenko, D.E. / Timofeev, V.I. / Britikov, V.V. / Britikova, E.V. / Kleymenov, S.Y. / Vlaskina, A.V. / Kuranova, I.P. / Mikhailova, A.G. / Rakitina, T.V.
History
DepositionApr 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
SupersessionNov 2, 2022ID: 6TF5
Revision 1.1Nov 2, 2022Group: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_radiation_wavelength / pdbx_database_PDB_obs_spr
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)79,4726
Polymers78,4601
Non-polymers1,0125
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint17 kcal/mol
Surface area29320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.210, 101.020, 108.890
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.: 5 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 52.07 %
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: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.7937 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: 0.7937 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 55364 / % possible obs: 99.9 % / Redundancy: 7.844 % / CC1/2: 0.99 / Net I/σ(I): 23.3
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 5.45 / Num. unique obs: 7214 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XE4

2xe4


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.141 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 2760 5 %RANDOM
Rwork0.206 ---
obs0.2082 52370 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.78 Å2 / Biso mean: 28.432 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 70 216 5831
Biso mean--64.75 26.19 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135766
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175249
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.6547811
X-RAY DIFFRACTIONr_angle_other_deg1.3291.58412077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.675678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22322.429354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63915925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2041541
X-RAY DIFFRACTIONr_chiral_restr0.0760.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021409
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 200 -
Rwork0.234 3799 -
all-3999 -
obs--99.7 %

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