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- PDB-1lvy: PORCINE ELASTASE -

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Basic information

Entry
Database: PDB / ID: 1lvy
TitlePORCINE ELASTASE
ComponentsELASTASE
KeywordsSERINE PROTEASE / HYDROLASE / ZYMOGEN / PANCREAS
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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.87 Å
AuthorsSchiltz, M. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: High-pressure krypton gas and statistical heavy-atom refinement: a successful combination of tools for macromolecular structure determination.
Authors: Schiltz, M. / Shepard, W. / Fourme, R. / Prange, T. / de la Fortelle, E. / Bricogne, G.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1978
Title: The Atomic Structure of Crystalline Porcine Pancreatic Elastase at 2.5 A Resolution: Comparisons with the Structure of Alpha-Chymotrypsin
Authors: Sawyer, L. / Shotton, D.M. / Campbell, J.W. / Wendell, P.L. / Muirhead, H. / Watson, H.C.
#3: Journal: Nature / Year: 1970
Title: Amino-Acid Sequence of Porcine Pancreatic Elastase and its Homologies with Other Serine Proteinases
Authors: Shotton, D.M. / Hartley, B.S.
History
DepositionJul 20, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)26,0643
Polymers25,9281
Non-polymers1362
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.637, 57.973, 75.320
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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE NUMBERING SCHEME USED FOR ELASTASE WAS CHOSEN TO MAXIMIZE HOMOLOGY WITH THE NUMBERING ...THE RESIDUE NUMBERING SCHEME USED FOR ELASTASE WAS CHOSEN TO MAXIMIZE HOMOLOGY WITH THE NUMBERING FOR CHYMOTRYPSINOGEN A.

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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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growpH: 5.5 / Details: CRYSTALLIZED IN NA2SO4 SOLUTION, pH 5.5
Crystal grow
*PLUS
Temperature: 291 K / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 Macetate11
212Na2SO4

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 0.863
DetectorType: J.HENDRIX,A.LENTFER / Detector: 'BLACK BOX' PROTOTYPE IMAGE PLATE / Date: Jul 14, 1995 / Details: IR-COATED CYLINDRICAL MIR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.863 Å / Relative weight: 1
ReflectionResolution: 1.87→30.4 Å / Num. obs: 17752 / % possible obs: 92.9 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 14.75 Å2 / Rmerge(I) obs: 0.022 / Net I/σ(I): 121
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 63.9 / % possible all: 78.6
Reflection
*PLUS
Num. measured all: 74579
Reflection shell
*PLUS
% possible obs: 78.6 % / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA(CCP4)data scaling
SHARPphasing
PROLSQrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS
Starting model: PDB ENTRY 3EST

3est


Resolution: 1.87→10 Å / Cross valid method: FREE-R / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.229 880 5 %
Rwork0.187 --
all0.206 17752 -
obs0.185 17598 93 %
Displacement parametersBiso mean: 15.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.87→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 6 79 1907
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0530.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.312.5
X-RAY DIFFRACTIONp_mcangle_it3.013
X-RAY DIFFRACTIONp_scbond_it3.412.5
X-RAY DIFFRACTIONp_scangle_it5.273
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.190.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2930.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2160.3
X-RAY DIFFRACTIONp_planar_tor2.93
X-RAY DIFFRACTIONp_staggered_tor17.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.920
X-RAY DIFFRACTIONp_special_tor

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