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- PDB-1h9l: PORCINE PANCREATIC ELASTASE COMPLEXED WITH ACETYL-VAL-GLU-PRO-ILE-COOH -

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Basic information

Entry
Database: PDB / ID: 1h9l
TitlePORCINE PANCREATIC ELASTASE COMPLEXED WITH ACETYL-VAL-GLU-PRO-ILE-COOH
Components
  • ELASTASE
  • PEPTIDE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / 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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsWright, P.A. / Wilmouth, R.C. / Clifton, I.J. / Schofield, C.J.
Citation
Journal: Eur.J.Biochem. / Year: 2001
Title: Kinetic and Crystallographic Analysis of Complexes Formed between Elastase and Peptides from Beta-Casein
Authors: Wright, P.A. / Wilmouth, R.C. / Clifton, I.J. / Schofield, C.J.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a Specific Acyl-Enzyme Complex Formed between Beta-Casomorphin-7 and Porcine Pancreatic Elastase
Authors: Wilmouth, R.C. / Clifton, I.J. / Robinson, C.V. / Roach, P.L. / Aplin, R.T. / Westwood, N.J. / Hajdu, J. / Schofield, C.J.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65A Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
#3: Journal: Biochem.J. / Year: 2000
Title: Ph-Jump Crystallographic Analyses of Gamma-Lactam-Porcine Pancreatic Elastase Complexes
Authors: Wright, P.A. / Wilmouth, R.C. / Clifton, I.J. / Schofield, C.J.
History
DepositionMar 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2001Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Revision 1.3Dec 13, 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE INHIBITOR
B: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5474
Polymers26,4112
Non-polymers1362
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.160, 57.840, 74.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide PEPTIDE INHIBITOR


Mass: 482.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS AN ESTER BOND BETWEEN THE CARBOXYL TERMINUS OF THE ACETYL-VAL-GLU-PRO-ILE PEPTIDE AND THE ...THERE IS AN ESTER BOND BETWEEN THE CARBOXYL TERMINUS OF THE ACETYL-VAL-GLU-PRO-ILE PEPTIDE AND THE HYDROXYL SIDE CHAIN OF SER-195
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: 1.83 Å3/Da / Density % sol: 32.15 %
Crystal growpH: 5
Details: CRYSTALS PREPARED FROM 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND THEN SOAKED WITH ACETYL-VAL-GLU-PRO-ILE (17 MG/ML) DISSOLVED IN SODIUM ACETATE (PH 5.0, 50MM) AND ...Details: CRYSTALS PREPARED FROM 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND THEN SOAKED WITH ACETYL-VAL-GLU-PRO-ILE (17 MG/ML) DISSOLVED IN SODIUM ACETATE (PH 5.0, 50MM) AND SODIUM SULPHATE (25 MM)
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mg/mlPPE1drop
250 mMsodium acetate1droppH5.0
350 mM1reservoirNa2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.67→22.9 Å / Num. obs: 24944 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15
Reflection shellResolution: 1.67→1.7 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 10 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 156137
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QIX

1qix


Resolution: 1.67→22.9 Å / SU B: 1.841 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.102
Details: THE STRUCTURE WAS REFINED WITHOUT ANGLE OR PLANARITY RESTRAINTS ON THE ESTER BOND BETWEEN SER- 195 AND THE PEPTIDE ISOLEUCINE.THE N-TERMINAL ACETYL GROUP OF THE PEPTIDE WAS DISORDERED AND ...Details: THE STRUCTURE WAS REFINED WITHOUT ANGLE OR PLANARITY RESTRAINTS ON THE ESTER BOND BETWEEN SER- 195 AND THE PEPTIDE ISOLEUCINE.THE N-TERMINAL ACETYL GROUP OF THE PEPTIDE WAS DISORDERED AND HENCE IS MISSING FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1019 4 %RANDOM
Rwork0.158 ---
obs0.159 24944 95.2 %-
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--0.39 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.67→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 6 233 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.021
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1320.5
X-RAY DIFFRACTIONp_mcbond_it1.2531.5
X-RAY DIFFRACTIONp_mcangle_it2.0092
X-RAY DIFFRACTIONp_scbond_it2.7143
X-RAY DIFFRACTIONp_scangle_it4.1014.5
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.150.2
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor13.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.420
X-RAY DIFFRACTIONp_special_tor015
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it2

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