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- PDB-8b53: Structure of porcine pancreatic elastase bound to a fragment of a... -

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Basic information

Entry
Database: PDB / ID: 8b53
TitleStructure of porcine pancreatic elastase bound to a fragment of a 4-azaindole inhibitor
ComponentsChymotrypsin-like elastase family member 1
KeywordsHYDROLASE / elastase / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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
3-methylbenzoic acid / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å
AuthorsFerraroni, M. / Gerace, A.
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 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)29,2105
Polymers28,8451
Non-polymers3644
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-17 kcal/mol
Surface area10560 Å2
Unit cell
Length a, b, c (Å)50.019, 57.910, 74.519
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 333 molecules

#2: Chemical ChemComp-OVV / 3-methylbenzoic acid


Mass: 136.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.81 Å3/Da / Density % sol: 31.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: sodium sulfate, 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: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.25→22.25 Å / Num. obs: 60617 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.032 / Rrim(I) all: 0.108 / Net I/σ(I): 11.3 / Num. measured all: 685669 / Scaling rejects: 20516
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.25-1.2710.80.4113190629490.9320.130.4324.1100
6.85-22.259.80.0742264310.9950.0220.07319.997.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1QNJ

1qnj


Resolution: 1.25→22.25 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.975 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0345 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1354 3007 5 %RANDOM
Rwork0.1123 ---
obs0.1135 57536 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.82 Å2 / Biso mean: 11.145 Å2 / Biso min: 3.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20 Å2
2--0.19 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.25→22.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 21 329 2169
Biso mean--20.07 28.62 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0121921
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151752
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.632634
X-RAY DIFFRACTIONr_angle_other_deg1.6221.5724003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6825248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30721.75397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65415283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5171513
X-RAY DIFFRACTIONr_chiral_restr0.1250.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022361
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02485
X-RAY DIFFRACTIONr_rigid_bond_restr2.8233673
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.157 214 -
Rwork0.142 4189 -
all-4403 -
obs--100 %

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