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- PDB-3hgp: Structure of porcine pancreatic elastase complexed with a potent ... -

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Basic information

Entry
Database: PDB / ID: 3hgp
TitleStructure of porcine pancreatic elastase complexed with a potent peptidyl inhibitor FR130180 determined by high resolution crystallography
ComponentsElastase-1
KeywordsHYDROLASE / Chymotrypsin Family / Serine Protease / Calcium / Disulfide bond / Metal-binding / Protease / Secreted / Zymogen
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-FRW / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 0.94 Å
AuthorsTamada, T. / Kinoshita, T. / Kuroki, R. / Tada, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Combined High-Resolution Neutron and X-ray Analysis of Inhibited Elastase Confirms the Active-Site Oxyanion Hole but Rules against a Low-Barrier Hydrogen Bond
Authors: Tamada, T. / Kinoshita, T. / Kurihara, K. / Adachi, M. / Ohhara, T. / Imai, K. / Kuroki, R. / Tada, T.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5794
Polymers25,9291
Non-polymers6503
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.859, 57.049, 74.333
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-1 /


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Porcine Pancreatic / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-FRW / 4-[[(2S)-3-methyl-1-oxo-1-[(2S)-2-[[(3S)-1,1,1-trifluoro-4-methyl-2-oxo-pentan-3-yl]carbamoyl]pyrrolidin-1-yl]butan-2-yl]carbamoyl]benzoic acid


Mass: 513.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30F3N3O6
#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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.3M sodium sulphate, 0.05M sodium acetate, pH5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 0.94→45.17 Å / Num. all: 134132 / Num. obs: 134132 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 26.4
Reflection shellResolution: 0.94→0.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.7 / Num. unique all: 12058 / % possible all: 80

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 1MMJ

1mmj


Resolution: 0.94→10 Å / Num. parameters: 20623 / Num. restraintsaints: 24325 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.128 6746 -RANDOM
Rwork0.107 ---
all-127267 --
obs-127267 92.6 %-
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 1791 / Occupancy sum non hydrogen: 2278
Refinement stepCycle: LAST / Resolution: 0.94→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 71 414 4095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0376
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.154
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.087
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.121

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