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- PDB-1qnj: THE STRUCTURE OF NATIVE PORCINE PANCREATIC ELASTASE AT ATOMIC RES... -

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Basic information

Entry
Database: PDB / ID: 1qnj
TitleTHE STRUCTURE OF NATIVE PORCINE PANCREATIC ELASTASE AT ATOMIC RESOLUTION (1.1 A)
ComponentsELASTASE
KeywordsHYDROLASE (SERINE PROTEASE) / HYDROLASE(SERINE PROTEASE) / ATOMIC RESOLUTION
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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsWurtele, M. / Hahn, M. / Hilpert, K. / Hohne, W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Atomic Resolution Structure of Native Porcine Pancreatic Elastase at 1.1 A
Authors: Wurtele, M. / Hahn, M. / Hilpert, K. / Hohne, W.
#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.W. / Clifton, I.J. / Pritchard, G.J. / Aplin, R.T. / Schofield, C.J.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65 Angstroms Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
#3: Journal: J.Mol.Biol. / Year: 1978
Title: The Atomic Structure of Crystalline Porcine Pancreatic Elastase at 2.5 Angstroms 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. / Diamond, R. / Ladner, R.C.
#4: Journal: Nature / Year: 1970
Title: Three-Dimensional Fourier Synthesis of Tosyl-Elastase at 3.5 Angstroms Resolution
Authors: Watson, H.C. / Shotton, D.M. / Cox, J.M. / Muirhead, H.
History
DepositionOct 15, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: pdbx_seq_map_depositor_info / refine
Item: _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _refine.pdbx_ls_cross_valid_method
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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_ptnr2_label_alt_id / _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

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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)26,1444
Polymers25,9291
Non-polymers2153
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.910, 57.820, 74.270
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


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PORCINE PANCREATIC ELASTASE / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE NUMBERING FOLLOWS THE NUMBERING OF BOVINE CHYMOTRYPSINOGEN A. THE RESIDUE ASN-77 OF ...RESIDUE NUMBERING FOLLOWS THE NUMBERING OF BOVINE CHYMOTRYPSINOGEN A. THE RESIDUE ASN-77 OF REFERENCE STRUCTURES WAS CHANGED TO ASP-77 IN ORDER TO MATCH WITH DNA SEQUENCE ENTRIES.

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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: 2.06 Å3/Da / Density % sol: 32.6 %
Crystal growTemperature: 291 K / pH: 8 / Details: 0.25 M NA2SO4 18 DEGREES CELSIUS, pH 8.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.25 M1dropNa2SO4
240 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.1→45.6 Å / Num. obs: 81820 / % possible obs: 92.7 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.9
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.02 / % possible all: 60.4
Reflection
*PLUS
Num. measured all: 1071726
Reflection shell
*PLUS
% possible obs: 60.4 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BTU

1btu


Resolution: 1.1→45.6 Å / Num. parameters: 19897 / Num. restraintsaints: 24006 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1652 4088 5.3 %RANDOM
obs0.1267 -88.2 %-
all-77673 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 23 / Occupancy sum hydrogen: 1762 / Occupancy sum non hydrogen: 2177
Refinement stepCycle: LAST / Resolution: 1.1→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 364 2197
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0289
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.088
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0.103
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1267
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.0289

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