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- PDB-1e38: PORCINE PANCREATIC ELASTASE COMPLEXED WITH (3S, 4S)N-PARA-NITROBE... -

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Basic information

Entry
Database: PDB / ID: 1.0E+38
TitlePORCINE PANCREATIC ELASTASE COMPLEXED WITH (3S, 4S)N-PARA-NITROBENZENESULPHONYL -3-ETHYL-4-(CARBOXYLIC ACID)PYRROLIDIN-2-ONE SOAKED IN PH 9 BUFFER FOR 2 MINUTES
ComponentsELASTASE
KeywordsSERINE PROTEASE / HYDROLASE / SERINE PROTEINASE
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-TPY / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWright, P.A. / Wilmouth, R.C. / Clifton, I.J. / Schofield, C.J.
Citation
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.
#1: Journal: Biochemistry / Year: 1999
Title: Mechanistic Insights Into the Inhibition of Serine Proteases by Monocyclic Lactams
Authors: Wilmouth, R.C. / Kassamally, S. / Westwood, N.J. / Sheppard, R.J. / Claridge, T.D.W. / Aplin, R.T. / Wright, P.A. / Pritchard, G.J. / Schofield, C.J.
#2: Journal: Biochemistry / Year: 1998
Title: Inhibition of Elastase by N-Sulfonylaryl Beta-Lactams: Anatomy of a Stable Acyl-Enzyme Complex
Authors: Wilmouth, R.C. / Westwood, N.J. / Anderson, K. / Brownlee, W. / Claridge, T.D.W. / Clifton, I.J. / Pritchard, G.J. / Aplin, R.T. / Schofield, C.J.
#3: 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.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65 A Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
History
DepositionJun 6, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 6, 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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
B: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4094
Polymers25,9281
Non-polymers4803
Water2,702150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.070, 57.910, 75.590
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 ELASTASE / PPE (PORCINE PANCREATIC ELASTASE)


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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TPY / (2S,3S)-3-FORMYL-2-({[(4-NITROPHENYL)SULFONYL]AMINO}METHYL)PENTANOIC ACID


Mass: 344.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O7S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE USED FOR THIS STRUCTURE IS THE SAME AS THAT OF NATIVE PORCINE PANCREATIC ELASTASE (3EST).

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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: 2.05 Å3/Da / Density % sol: 30.1 %
Crystal growpH: 9
Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE, PH 5.0; THEN SOAKED IN 25 MM SODIUM SULPHATE, 50MM SODIUM ACETATE, 20 MG/ML GAMMA-LACTAM, 10% (V/V) DMSO, PH 5.0 FOR 24 HOURS
Crystal grow
*PLUS
pH: 5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
250 mMsodium acetate11
325 mMsodium sulfate11
425 mg/mlPPE11
510 %(v/v)DMSO11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.826
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826 Å / Relative weight: 1
ReflectionResolution: 1.7→18.3 Å / Num. obs: 24440 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 5.74 / % possible all: 95.4
Reflection shell
*PLUS
% possible obs: 95.4 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EST

3est


Resolution: 1.7→18.3 Å / SU B: 2.02 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114 / Details: SHELX ALSO USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1011 4 %RANDOM
Rwork0.183 ---
obs-24440 98.5 %-
Displacement parametersBiso mean: 18.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.169 Å20.368 Å20 Å2
2--0 Å2-0.533 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 29 150 2001
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2522
X-RAY DIFFRACTIONp_mcangle_it1.76983
X-RAY DIFFRACTIONp_scbond_it1.7052
X-RAY DIFFRACTIONp_scangle_it2.6163
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1210.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2470.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1290.3
X-RAY DIFFRACTIONp_planar_tor3.67
X-RAY DIFFRACTIONp_staggered_tor13.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.720
X-RAY DIFFRACTIONp_special_tor015

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