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- PDB-1eja: STRUCTURE OF PORCINE TRYPSIN COMPLEXED WITH BDELLASTASIN, AN ANTI... -

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Basic information

Entry
Database: PDB / ID: 1eja
TitleSTRUCTURE OF PORCINE TRYPSIN COMPLEXED WITH BDELLASTASIN, AN ANTISTASIN-TYPE INHIBITOR
Components
  • BDELLASTASIN
  • TRYPSIN
KeywordsHYDROLASE/INHIBITOR / Complex (Hydrolase-Inhibitor) / Hydrolase / Inhibitor / Bdellastasin / Antistasin / Trypsin / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Antistasin; domain 1 / Antistasin; domain 1 / Antistasin-like domain / Antistasin family / Antistasin-like domain profile. / Hirudin/antistatin / : / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Antistasin; domain 1 / Antistasin; domain 1 / Antistasin-like domain / Antistasin family / Antistasin-like domain profile. / Hirudin/antistatin / : / Ribbon / 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
Trypsin / Bdellastasin
Similarity search - Component
Biological speciesHirudo medicinalis (medicinal leech)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsRester, U. / Moser, M. / Huber, R. / Bode, W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: L-Isoaspartate 115 of porcine beta-trypsin promotes crystallization of its complex with bdellastasin.
Authors: Rester, U. / Moser, M. / Huber, R. / Bode, W.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Structure of the Complex of the Antistasin-type Inhibitor Bdellastasin with Trypsin and Modelling of the Bdellastasin-microplasmin System
Authors: Rester, U. / Bode, W. / Moser, M. / Parry, M.A. / Huber, R. / Auerswald, E.
#2: Journal: Eur.J.Biochem. / Year: 1998
Title: Bdellastasin, a serine protease inhibitor of the antistasin family from the medical leech (Hirudo medicinalis) - primary structure, expression in yeast, and characterization of native and recombinant inhibitor.
Authors: Moser, M. / Auerswald, E. / Mentele, R. / Eckerskorn, C. / Fritz, H. / Fink, E.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_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: TRYPSIN
B: BDELLASTASIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8683
Polymers29,8452
Non-polymers231
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.020, 70.020, 119.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TRYPSIN


Mass: 23493.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: LYOPHILIZED PORCINE PANCREATIC B-TRYPSIN TYPEIX (E.C. 3.4.21.4) PURCHASED FROM SIGMA.
Source: (natural) Sus scrofa (pig) / Tissue: PANCREAS / References: UniProt: P00761, trypsin
#2: Protein BDELLASTASIN


Mass: 6351.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): S78 / References: UniProt: P82107
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 4.0 M Na-formate, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM1dropNaCl
250 mMMES1drop
310 mg/mlprotein1drop
4150 mM1reservoirNaCl
520 mMMES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→34.9 Å / Num. all: 51140 / Num. obs: 8636 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.094
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6 % / Rmerge(I) obs: 0.353 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 51140
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
CNSrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.7→8 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 848 RANDOM
Rwork0.191 --
all-8272 -
obs-7989 -
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 1 255 2748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.546
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.01
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.777

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