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- PDB-7ne4: E125A mutant of oligopeptidase B from S. proteomaculans with modi... -

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Basic information

Entry
Database: PDB / ID: 7ne4
TitleE125A mutant of oligopeptidase B from S. proteomaculans with modified hinge region
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 / Oligopeptidase B
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.717 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: 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
DepositionFeb 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oligopeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8714
Polymers78,2641
Non-polymers6073
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint9 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.840, 98.560, 108.260
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: 78263.664 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 / Spermine


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


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
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: 0.8 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: 2.717→44.9 Å / Num. obs: 20453 / % possible obs: 99.92 % / Redundancy: 6.18 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 8.45
Reflection shellResolution: 2.717→2.79 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 1476

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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: 2.717→44.85 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.829 / SU B: 44.184 / SU ML: 0.412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3056 1023 5 %RANDOM
Rwork0.25 ---
obs0.2527 19430 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 65.54 Å2 / Biso mean: 28.828 Å2 / Biso min: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å2-0 Å20 Å2
2--0.83 Å2-0 Å2
3----2.5 Å2
Refinement stepCycle: final / Resolution: 2.717→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 42 50 5623
Biso mean--50.87 31.62 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0175715
X-RAY DIFFRACTIONr_bond_other_d0.0010.0195184
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.8517752
X-RAY DIFFRACTIONr_angle_other_deg0.9042.62511923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54922.393351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34315920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5741541
X-RAY DIFFRACTIONr_chiral_restr0.0580.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021404
LS refinement shellResolution: 2.717→2.788 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.429 74 -
Rwork0.33 1408 -
obs--99.87 %

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