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- PDB-8b04: STRUCTURE OF PORCINE PANCREATIC ELASTASE BOUND TO A FRAGMENT OF A... -

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Basic information

Entry
Database: PDB / ID: 8b04
TitleSTRUCTURE OF PORCINE PANCREATIC ELASTASE BOUND TO A FRAGMENT OF AN ISOXAZOLONE INHIBITOR
ComponentsChymotrypsin-like elastase family member 1
KeywordsLYASE / CHYMOTRYPSIN FAMILY / SERINE PROTEASE
Function / homology
Function and homology information


pancreatic elastase / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-OU0 / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFerraroni, M. / Giovannoni, P. / Masini, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Struct. / Year: 2023
Title: X-ray structural study of human neutrophil elastase inhibition with a series of azaindoles, azaindazoles and isoxazolones
Authors: Gerace, A. / Masini, V. / Crocetti, L. / Giovannoni, M.P. / Ferraroni, M.
History
DepositionSep 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chymotrypsin-like elastase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2375
Polymers28,8451
Non-polymers3924
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-8 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.220, 58.640, 74.910
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 Chymotrypsin-like elastase family member 1 / Elastase-1 / PORCINE PANCREATIC ELASTASE


Mass: 28845.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-OU0 / 2-cyclopropylcarbonyl-3-propan-2-yl-1,2-oxazol-5-one


Mass: 195.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.88 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: sodium sulphate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 30354 / % possible obs: 99.4 % / Redundancy: 12.307 % / Biso Wilson estimate: 29.181 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.124 / Χ2: 0.868 / Net I/σ(I): 16.12 / Num. measured all: 373577 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.6412.5731.3982.2627358220621760.7881.45698.6
1.64-1.6912.531.1332.8526952217521510.8191.18198.9
1.69-1.7312.2810.9663.4125533210320790.8761.00798.9
1.73-1.7912.2160.7414.6524909205320390.9450.77399.3
1.79-1.8512.4550.5976.3724511198319680.9590.62399.2
1.85-1.9112.0430.5088.0722990192019090.9770.5399.4
1.91-1.9812.7290.39411.0423702187418620.9890.41199.4
1.98-2.0612.5050.34313.3522446180117950.990.35799.7
2.06-2.1612.0630.2816.2420724172617180.9940.29299.5
2.16-2.2612.4580.25118.3920444164916410.9950.26299.5
2.26-2.3812.0320.19821.418854156915670.9930.20799.9
2.38-2.5313.1570.17423.3919643149714930.9960.18199.7
2.53-2.712.8010.13726.0518177142114200.9970.14399.9
2.7-2.9212.180.10829.2916005131413140.9970.112100
2.92-3.212.3970.08432.5414988121212090.9970.08899.8
3.2-3.5712.3280.0735.4213647111011070.9980.07399.7
3.57-4.1311.9640.0637.731195210009990.9980.06399.9
4.13-5.0611.3390.05638.595028408380.9980.05999.8
5.06-7.1511.0420.05636.7573766726680.9980.05999.4
7.15-309.6360.05335.2738644044010.9960.05699.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HGP

3hgp


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.572 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0852 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 1503 5 %RANDOM
Rwork0.1719 ---
obs0.1727 28825 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.93 Å2 / Biso mean: 24.306 Å2 / Biso min: 13.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å2-0 Å2
2---0.59 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 14 116 1940
Biso mean--37.76 32.51 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121871
X-RAY DIFFRACTIONr_angle_refined_deg1.891.6272559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73422.28392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02315270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6341511
X-RAY DIFFRACTIONr_chiral_restr0.1290.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021434
LS refinement shellResolution: 1.6→1.64 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.312 116 -
Rwork0.254 2051 -
obs--98.63 %

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