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- PDB-7zjz: catalytically non active S532A mutant of oligopeptidase B from S.... -

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Basic information

Entry
Database: PDB / ID: 7zjz
Titlecatalytically non active S532A mutant of oligopeptidase B from S. proteomaculans
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: 1.9 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: Crystals / Year: 2022
Title: Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation
Authors: Britikov, V.V. / Timofeev, V.I. / Petrenko, D.E. / Britikova, E.V. / Nikolaeva, A.Y. / Vlaskina, A.V. / Boyko, K.M. / Mikhailova, A.G. / Rakitina, T.V.
History
DepositionApr 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 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)79,1925
Polymers78,3831
Non-polymers8094
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint12 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.860, 100.450, 108.920
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 / / Prolyl oligopeptidase family serine peptidase


Mass: 78382.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (bacteria) / Gene: opdB, JKX24_00380 / Production host: Escherichia coli (E. coli) / References: UniProt: B3VI58
#2: Chemical
ChemComp-SPM / SPERMINE / Spermine


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


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 277 K / Method: counter-diffusion
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: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 63693 / % possible obs: 99.96 % / Redundancy: 7.15 % / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.124 / Net I/σ(I): 3.3271
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 9183 / Rrim(I) all: 0.61 / % possible all: 100

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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: 6TF5

6tf5
PDB Unreleased entry


Resolution: 1.9→29.44 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.598 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 3146 4.9 %RANDOM
Rwork0.1974 ---
obs0.2 60473 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.06 Å2 / Biso mean: 40.059 Å2 / Biso min: 19.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.9→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 0 56 368 5963
Biso mean--70.25 44.56 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135746
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155228
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6547790
X-RAY DIFFRACTIONr_angle_other_deg1.3221.58312028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6745678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1822.345354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72815925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.121542
X-RAY DIFFRACTIONr_chiral_restr0.0760.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021405
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 216 -
Rwork0.357 4396 -
all-4612 -
obs--99.98 %

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