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- PDB-1c9p: COMPLEX OF BDELLASTASIN WITH PORCINE TRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1c9p
TitleCOMPLEX OF BDELLASTASIN WITH PORCINE TRYPSIN
Components
  • BDELLASTASIN
  • TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / COMPLEX (HYDROLASE-INHIBITOR) / HYDROLASE / INHIBITOR / ANTISTASIN / PLASMIN / ISOASPARTATE / HYDROLASE-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 / Peptidase S1A, chymotrypsin family ...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 / 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
Trypsin / Bdellastasin
Similarity search - Component
Biological speciesHirudo medicinalis (medicinal leech)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsRester, U.
Citation
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.
#1: 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 characterisation of native and recombinant inhibitor.
Authors: Moser, M. / Auerswald, E. / Mentele, R. / Eckerskorn, C. / Fritz, H. / Fink, E.
#2: 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.
History
DepositionAug 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues ...pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / software
Revision 1.5Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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_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_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_leaving_atom_flag / _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

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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)29,8863
Polymers29,8462
Non-polymers401
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-21 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.330, 63.330, 130.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein TRYPSIN / / E.C.3.4.21.4


Mass: 23494.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Secretion: SALIVA
Keywords: ISOASPARTATE115 RESULTS FROM A SPONTANEOUS DEAMIDATION, ACCOMPANIED BY A SIMULTANEOUS ISOMERISATION REACTION
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) / References: UniProt: P82107
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 10% 2-PROPANOL, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2150 mM1dropNaCl
320 mMMES1drop
410 %(v/v)2-propanol1reservoir
520 %(w/v)PEG40001reservoir
6100 mMHEPPS1reservoir

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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: May 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→10 Å / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.28 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 7063 / Redundancy: 5.9 % / Num. measured all: 31627
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
AMoREphasing
CNSrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
Details: ASP 115 HAS BEEN REFINED USING A NEW CREATED TOP AND PAR
RfactorNum. reflection% reflectionSelection details
Rfree0.227 697 10 %RANDOM
Rwork0.185 ---
all0.191 6676 --
obs0.19 6481 86.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 1 135 2140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.466
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d25.04
X-RAY DIFFRACTIONc_improper_angle_d0.716

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