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- PDB-1b0e: CRYSTAL STRUCTURE OF PORCINE PANCREATIC ELASTASE WITH MDL 101,146 -

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Basic information

Entry
Database: PDB / ID: 1b0e
TitleCRYSTAL STRUCTURE OF PORCINE PANCREATIC ELASTASE WITH MDL 101,146
ComponentsPROTEIN (ELASTASE)
KeywordsHYDROLASE / SERINE PROTEASE / FLUOROETHYL KETONES
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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-SEI / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchreuder, H.A. / Metz, W.A. / Peet, N.P. / Pelton, J.T. / Tardif, C.
CitationJournal: J.Med.Chem. / Year: 1998
Title: Inhibition of human neutrophil elastase. 4. Design, synthesis, X-ray crystallographic analysis, and structure-activity relationships for a series of P2-modified, orally active peptidyl pentafluoroethyl ketones.
Authors: Cregge, R.J. / Durham, S.L. / Farr, R.A. / Gallion, S.L. / Hare, C.M. / Hoffman, R.V. / Janusz, M.J. / Kim, H.O. / Koehl, J.R. / Mehdi, S. / Metz, W.A. / Peet, N.P. / Pelton, J.T. / ...Authors: Cregge, R.J. / Durham, S.L. / Farr, R.A. / Gallion, S.L. / Hare, C.M. / Hoffman, R.V. / Janusz, M.J. / Kim, H.O. / Koehl, J.R. / Mehdi, S. / Metz, W.A. / Peet, N.P. / Pelton, J.T. / Schreuder, H.A. / Sunder, S. / Tardif, C.
History
DepositionNov 9, 1998Processing site: RCSB
Revision 1.0Nov 18, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ELASTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6013
Polymers25,9281
Non-polymers6732
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.100, 69.100, 51.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein PROTEIN (ELASTASE) / PPE


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SEI / 1-{3-METHYL-2-[4-(MORPHOLINE-4-CARBONYL)-BENZOYLAMINO]-BUTYRYL}-PYRROLIDINE-2-CARBOXYLIC ACID (3,3,4,4,4-PENTAFLUORO-1-ISOPROPYL-2-OXO-BUTYL)-AMIDE / MDL 101,146


Mass: 632.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H37F5N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.71 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5
Details: SITTING DROP PROCEDURE. PROTEIN DROP: 13 MG/ML PPE (SERVA) 9.3 MM SODIUM ACETATE (PH 5.0), 22.4 MM SODIUM SULFATE, 2.2 MM MDL 103,139 IN DMF RESERVOIR: 10 MM SODIUM ACETATE (PH 5.0), 20 MM ...Details: SITTING DROP PROCEDURE. PROTEIN DROP: 13 MG/ML PPE (SERVA) 9.3 MM SODIUM ACETATE (PH 5.0), 22.4 MM SODIUM SULFATE, 2.2 MM MDL 103,139 IN DMF RESERVOIR: 10 MM SODIUM ACETATE (PH 5.0), 20 MM SODIUM SULFATE., vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
29.3 mMsodium acetate1drop
322.4 mMsodium sulfate1drop
42.2 mMMDL 1031391drop
510 mMsodium acetate1reservoir
620 mMsodium sulfate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 19, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 24302 / % possible obs: 93.4 % / Redundancy: 4.2 % / Rsym value: 0.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.4 % / Rsym value: 0.292 / % possible all: 83.2
Reflection
*PLUS
Num. measured all: 101240 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 83.2 % / Rmerge(I) obs: 0.292

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLORmodel building
X-PLOR3.1refinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EST

3est


Resolution: 1.8→8 Å / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.18 --
obs0.18 24038 95.9 %
Displacement parametersBiso mean: 21.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 45 197 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.051.5
X-RAY DIFFRACTIONx_mcangle_it4.852
X-RAY DIFFRACTIONx_scbond_it4.533
X-RAY DIFFRACTIONx_scangle_it7.595
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.44 2572 -
obs--81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2INHIBITOR.PAR103139.TOP
X-RAY DIFFRACTION3WAT.PARWAT.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31

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