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- PDB-1an1: LEECH-DERIVED TRYPTASE INHIBITOR/TRYPSIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1an1
TitleLEECH-DERIVED TRYPTASE INHIBITOR/TRYPSIN COMPLEX
Components
  • TRYPSIN
  • TRYPTASE INHIBITOR
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / SERINE PROTEINASE INHIBITOR / TRYPTASE INHIBITION / NON-CLASSICAL KAZAL-TYPE INHIBITOR / COMPLEX (SERINE PROTEASE-INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Trypsin / Leech-derived tryptase inhibitor C
Similarity search - Component
Biological speciesSus scrofa (pig)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPriestle, J.P. / Di Marco, S.
Citation
Journal: Structure / Year: 1997
Title: Structure of the complex of leech-derived tryptase inhibitor (LDTI) with trypsin and modeling of the LDTI-tryptase system.
Authors: Di Marco, S. / Priestle, J.P.
#1: Journal: Eur.J.Biochem. / Year: 1996
Title: Purification, Characterization and Biological Evaluation of Recombinant Leech-Derived Tryptase Inhibitor (Rldti) Expressed at High Level in the Yeast Saccharomyces Cerevisiae
Authors: Pohlig, G. / Fendrich, G. / Knecht, R. / Eder, B. / Piechottka, G. / Sommerhoff, C.P. / Heim, J.
#2: Journal: Biol.Chem.Hoppe-Seyler / Year: 1994
Title: A Kazal-Type Inhibitor of Human Mast Cell Tryptase: Isolation from the Medical Leech Hirudo Medicinalis, Characterization, and Sequence Analysis
Authors: Sommerhoff, C.P. / Sollner, C. / Mentele, R. / Piechottka, G.P. / Auerswald, E.A. / Fritz, H.
History
DepositionJun 26, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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

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Assembly

Deposited unit
E: TRYPSIN
I: TRYPTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2853
Polymers28,2452
Non-polymers401
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-22 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.700, 63.700, 130.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11E-393-

HOH

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Components

#1: Protein TRYPSIN / / LDTI


Mass: 23494.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00761
#2: Protein/peptide TRYPTASE INHIBITOR


Mass: 4750.614 Da / Num. of mol.: 1 / Mutation: N115D (D-ASPARTIC ACID FORM)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Organ: SALIVARY GLANDS / Plasmid: PDP34 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): H449 / Variant (production host): TR1376, TR1417 / References: UniProt: P80424, trypsin
#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.: 138 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 8.5
Details: 30% V/V 2-PROPANOL, 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, PH 8.5 ROOM TEMPERATURE 27 MONTHS FOR GROWTH.
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %(v/v)2-propanol1reservoir
20.2 Mammonium acetate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 29, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→29.14 Å / Num. obs: 17213 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 8.73 % / Rmerge(I) obs: 0.1154 / Rsym value: 0.1154 / Net I/σ(I): 27.82
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4846 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.4846 / % possible all: 79.4
Reflection
*PLUS
Num. measured all: 150264
Reflection shell
*PLUS
% possible obs: 79.4 %

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Processing

Software
NameVersionClassification
XDSdata scaling
MARSCALEdata reduction
AMoREphasing
X-PLOR3.1refinement
XDSdata reduction
MARSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PORCINE PANCREATIC BETA-TRYPSIN (PDB ENTRY 1EPT)

1ept


Resolution: 2.03→6 Å / Rfactor Rfree error: 0.0076 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUE 115 WAS REFINED AS D-ASPARTIC ACID. WATER MOLECULE 98 IS LOCATED ON A CRYSTALLOGRAPHIC 2-FOLD AXIS AND THEREFORE HAS AN OCCUPANCY OF 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.228 909 5.5 %RANDOM
Rwork0.17 ---
obs0.17 16406 94.3 %-
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 2.03→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 1 138 2063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.978
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.75
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.481
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
LS refinement shellResolution: 2.03→2.09 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.298 68 4.8 %
Rwork0.267 15497 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSXD.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.ASD
X-RAY DIFFRACTION3PARAM19X.SUPTOPH19.WAT
X-RAY DIFFRACTION4TOPH19.CAL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.757
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.481

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