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- PDB-7ywz: Modified oligopeptidase B from S. proteomaculans in intermediate ... -

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Basic information

Entry
Database: PDB / ID: 7ywz
TitleModified oligopeptidase B from S. proteomaculans in intermediate conformation with 4 spermine molecules at 1.75 A resolution
ComponentsOligopeptidase B
KeywordsHYDROLASE
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: 1.75 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 4 spermine molecules at 1.75 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
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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)79,3616
Polymers78,4601
Non-polymers9015
Water10,124562
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint13 kcal/mol
Surface area29010 Å2
Unit cell
Length a, b, c (Å)72.890, 100.440, 108.550
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.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
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: 0.8 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: 1.75→30 Å / Num. obs: 80464 / % possible obs: 99.5 % / Redundancy: 4.96 % / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.075 / Net I/σ(I): 7.4706
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.87 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.53 / Num. unique obs: 11668 / Rrim(I) all: 0.38 / % possible all: 99.93

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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: 7OB1

7ob1


Resolution: 1.75→29.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.128 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 4062 5.1 %RANDOM
Rwork0.1719 ---
obs0.1735 76338 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.44 Å2 / Biso mean: 21.321 Å2 / Biso min: 9.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.75→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 62 562 6169
Biso mean--48.42 27.66 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135785
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155249
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.6537846
X-RAY DIFFRACTIONr_angle_other_deg1.4581.58312079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4425684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63322.472356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43915929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7911541
X-RAY DIFFRACTIONr_chiral_restr0.0830.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021419
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 292 -
Rwork0.204 5608 -
all-5900 -
obs--99.9 %

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