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- PDB-1qgf: PORCINE PANCREATIC ELASTASE COMPLEXED WITH (3R, 4S)N-PARA-TOLUENE... -

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Basic information

Entry
Database: PDB / ID: 1qgf
TitlePORCINE PANCREATIC ELASTASE COMPLEXED WITH (3R, 4S)N-PARA-TOLUENESULPHONYL-3-ETHYL-4-(CARBOXYLIC ACID)PYRROLIDIN-2-ONE
ComponentsELASTASE
KeywordsHYDROLASE / SERINE PROTEASE / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...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 domain profile. / Serine proteases, trypsin family, serine active site. / 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-TPX / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.7 Å
AuthorsWilmouth, R.C. / Kassamally, S. / Westwood, N.J. / Sheppard, R.J. / Claridge, T.D.W. / Wright, P.A. / Pritchard, G.J. / Schofield, C.J.
Citation
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. / Aplin, R.T. / Wright, P.A. / Pritchard, G.J. / Schofield, C.J.
#1: 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. / Clifton, I.J. / Pritchard, G.J. / Aplin, R.T. / Schofield, C.J.
#2: 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.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of native porcine pancreatic elastase at 1.65 A resolutions.
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
History
DepositionApr 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3784
Polymers25,9281
Non-polymers4503
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.220, 57.630, 74.480
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-TPX / (2S,3S)-3-FORMYL-2-({[(4-METHYLPHENYL)SULFONYL]AMINO}METHYL)PENTANOIC ACID


Mass: 313.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19NO5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTPX 280: COVALENTLY ATTACHED TO SER-195 VIA AN ESTER LINKAGE BETWEEN OG OF SER-195 AND C OF THE ...TPX 280: COVALENTLY ATTACHED TO SER-195 VIA AN ESTER LINKAGE BETWEEN OG OF SER-195 AND C OF THE GAMMA-LACTAM; THE GAMMA-LACTAM IS RING-OPENED IN THE PROCESS. THE TOLUENESULPHONYL RING WAS POORLY DEFINED SO THE POSITION OF THE TOSYL RING WAS MODELLED INTO THE STRUCTURE USING THE LOCATION OXYGEN ATOMS OF THE SULPHONAMIDE AND THE ELECTRON DENSITY VISIBLE FOR THE CARBON ATOM IN THE PHENYL RING NEAREST THE SULPHUR ATOM AS A GUIDE BUT THE OCCUPANCY OF THE ATOMS WAS SET TO ZERO.
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: 5
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, pH 5.00
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDUnitCommon nameCrystal-IDSol-ID
1mg/mlalpha-lactam11
2mMsodium acetate11
3mMsodium sulfate11
4mg/mlPPE11
5%(v/v)DMSO11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: YALE-TYPE MIRRORS
RadiationMonochromator: NICKEL FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20.76 Å / Num. obs: 23759 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.88 % / Biso Wilson estimate: 13.94 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.82
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 12.12 / % possible all: 95.2
Reflection
*PLUS
% possible obs: 97.6 % / Num. measured all: 153319
Reflection shell
*PLUS
% possible obs: 95.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 3EST

3est


Resolution: 1.7→20.8 Å / SU B: 1.88 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.11 / Details: SHELX,CNS,XPLOR ALSO USED
RfactorNum. reflection% reflectionSelection details
Rfree0.21 941 4 %RANDOM
Rwork0.183 ---
obs-23759 97.6 %-
Displacement parametersBiso mean: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.066 Å20.321 Å20 Å2
2--0 Å2-1.08 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 27 159 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.03
X-RAY DIFFRACTIONp_angle_d0.0240.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7472
X-RAY DIFFRACTIONp_mcangle_it2.3033
X-RAY DIFFRACTIONp_scbond_it2.1962
X-RAY DIFFRACTIONp_scangle_it3.2983
X-RAY DIFFRACTIONp_plane_restr0.024
X-RAY DIFFRACTIONp_chiral_restr0.0850.15
X-RAY DIFFRACTIONp_singtor_nbd0.1690.3
X-RAY DIFFRACTIONp_multtor_nbd0.2340.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1080.3
X-RAY DIFFRACTIONp_planar_tor4.115
X-RAY DIFFRACTIONp_staggered_tor12.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.120
X-RAY DIFFRACTIONp_special_tor015

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