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- PDB-1bru: STRUCTURE OF PORCINE PANCREATIC ELASTASE COMPLEXED WITH THE ELAST... -

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Basic information

Entry
Database: PDB / ID: 1bru
TitleSTRUCTURE OF PORCINE PANCREATIC ELASTASE COMPLEXED WITH THE ELASTASE INHIBITOR GR143783
ComponentsELASTASE
KeywordsSERINE PROTEASE / HYDROLASE
Function / homology
Function and homology information


pancreatic elastase II / Formation of the cornified envelope / insulin catabolic process / regulation of platelet aggregation / regulation of insulin secretion / response to insulin / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region
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
2-(2-HYDROXY-CYCLOPENTYL)-PENT-4-ENAL / Chymotrypsin-like elastase family member 2A
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsJhoti, H. / Singh, O.M.P. / Wonacott, A.
CitationJournal: To be Published
Authors: Jhoti, H. / Singh, O.M.P. / Wonacott, A.
History
DepositionAug 24, 1998Processing site: BNL
Revision 1.0Aug 25, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0162
Polymers25,8481
Non-polymers1681
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.590, 46.450, 128.230
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: 25847.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: INHIBITOR GR143783 COVALENTLY ATTACHED TO PPE, BOND BETWEEN C 30 (INHIBITOR) AND OG SER 195
Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P08419, pancreatic elastase II
#2: Chemical ChemComp-1NB / 2-(2-HYDROXY-CYCLOPENTYL)-PENT-4-ENAL / GR143783


Mass: 168.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.4 Å3/Da / Density % sol: 48.64 %
Crystal growpH: 5 / Details: pH 5.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 8677 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
MADNESSdata collection
X-PLORrefinement
MADNESSdata reduction
RefinementResolution: 2.3→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.147 --
obs0.147 5000 98 %
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 12 194 2023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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