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- PDB-8uo7: Bovine trypsin in complex with deacetylated wild type microviridin J -

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Basic information

Entry
Database: PDB / ID: 8uo7
TitleBovine trypsin in complex with deacetylated wild type microviridin J
Components
  • Cationic trypsin
  • Deacetylated wildtype microviridin J
KeywordsHYDROLASE / Hydrolase inhibitor
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Microcystis aeruginosa MRC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, W. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Org.Lett. / Year: 2024
Title: Alternative Linkage Chemistries in the Chemoenzymatic Synthesis of Microviridin-Based Cyclic Peptides.
Authors: Patel, K.P. / Chen, W.T. / Delbecq, L. / Bruner, S.D.
History
DepositionOct 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
C: Deacetylated wildtype microviridin J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2515
Polymers25,0232
Non-polymers2283
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-31 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.650, 71.650, 72.976
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide Deacetylated wildtype microviridin J


Type: Cyclic peptide / Class: Enzyme inhibitor / Mass: 1698.830 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The last tryptophan is not observed in the crystal structure.
Source: (synth.) Microcystis aeruginosa MRC (bacteria) / References: BIRD: PRD_002533

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Non-polymers , 4 types, 70 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 295.37 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M sodium cacodylate pH 7.0, 0.2 M ammonium sulfate, 30%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.2→28.55 Å / Num. obs: 11366 / % possible obs: 99.87 % / Redundancy: 9.8 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1895 / Rrim(I) all: 0.2006 / Net I/σ(I): 8.34
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.8738 / Num. unique obs: 1120 / CC1/2: 0.883 / CC star: 0.968 / Rrim(I) all: 0.9234 / Χ2: 3.48 / % possible all: 99.91

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Processing

Software
NameVersionClassification
REFMAC8.0.013refinement
PHENIX1.19.2refinement
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 0.006 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25818 582 5.1 %RANDOM
Rwork0.19651 ---
obs0.19944 10797 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.453 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0.52 Å2-0 Å2
2---1.04 Å2-0 Å2
3---3.37 Å2
Refinement stepCycle: 1 / Resolution: 2.2→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 12 67 1811
LS refinement shellResolution: 2.2→2.255 Å
RfactorNum. reflection% reflection
Rfree0.305 40 -
Rwork0.248 788 -
obs--99.16 %

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