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- PDB-8ono: Modified oligopeptidase B from S. proteamaculans in intermediate ... -

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Basic information

Entry
Database: PDB / ID: 8ono
TitleModified oligopeptidase B from S. proteamaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution
ComponentsOligopeptidase B
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
: / Prolyl oligopeptidase, N-terminal domain / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold / Mainly Beta
Similarity search - Domain/homology
SPERMINE / Oligopeptidase B
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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: To Be Published
Title: Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution
Authors: Petrenko, D.E. / Boyko, K.M. / Nikolaeva, A.Y. / Vlaskina, A.V. / Mikhailova, A.G. / Timofeev, V.I. / Rakitina, T.V.
History
DepositionApr 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
Water9,656536
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint19 kcal/mol
Surface area29010 Å2
Unit cell
Length a, b, c (Å)73.090, 100.620, 108.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: Serratia proteamaculans (bacteria) / 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.: 536 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
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: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 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: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 95311 / % possible obs: 98.57 % / Redundancy: 5.84 % / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.056 / Net I/σ(I): 9.2633
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 13658 / Rrim(I) all: 0.359

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.806 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 4673 4.9 %RANDOM
Rwork0.18611 ---
obs0.18778 90588 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.035 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.65→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 70 536 6151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135764
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155249
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6547809
X-RAY DIFFRACTIONr_angle_other_deg1.4581.58412076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23622.408353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79815924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7971541
X-RAY DIFFRACTIONr_chiral_restr0.0890.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021409
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2342.1792712
X-RAY DIFFRACTIONr_mcbond_other2.2322.1792711
X-RAY DIFFRACTIONr_mcangle_it3.283.2683390
X-RAY DIFFRACTIONr_mcangle_other3.283.2693391
X-RAY DIFFRACTIONr_scbond_it3.0882.5573052
X-RAY DIFFRACTIONr_scbond_other3.0882.5583053
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6063.6934420
X-RAY DIFFRACTIONr_long_range_B_refined6.35926.276517
X-RAY DIFFRACTIONr_long_range_B_other6.32526.0076430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 305 -
Rwork0.213 6565 -
obs--97.49 %

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