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- PDB-1h9h: COMPLEX OF EETI-II WITH PORCINE TRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1h9h
TitleCOMPLEX OF EETI-II WITH PORCINE TRYPSIN
Components
  • TRYPSIN
  • TRYPSIN INHIBITOR II
KeywordsHYDROLASE INHIBITOR / COMPLEX (SERINE PROTEASE-INHIBITOR) / TRYPSIN / SQUASH INHIBITOR / CYSTINE KNOT / HYDROLASE
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
Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Plant trypsin inhibitors / Proteinase/amylase inhibitor domain superfamily / : / 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 ...Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Plant trypsin inhibitors / Proteinase/amylase inhibitor domain superfamily / : / 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 / Trypsin inhibitor 2
Similarity search - Component
Biological speciesSUS SCROFA (pig)
ECBALLIUM ELATERIUM (jumping cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKraetzner, R. / Wentzel, A. / Kolmar, H. / Uson, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Ecballium Elaterium Trypsin Inhibitor II (Eeti-II): A Rigid Molecular Scaffold
Authors: Kraetzner, R. / Debreczeni, J.E. / Pape, T. / Schneider, T.R. / Wentzel, A. / Kolmar, H. / Sheldrick, G.M. / Uson, I.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Sequence Requirements of the Gpng Beta-Turn of the Ecballium Elaterium Trypsin Inhibitor II Explored by Combinatorial Library Screening
Authors: Wentzel, A. / Christmann, A. / Kraetzner, R. / Kolmar, H.
#2: Journal: Biochemistry / Year: 1999
Title: Min-21 and Min-23, the Smallest Peptides that Fold Like a Cystine-Stabilized Beta-Sheet Motif: Design, Solution Structure, and Thermal Stability
Authors: Heitz, A. / Le-Nguyen, D. / Chiche, L.
#3: Journal: Proteins: Struct.,Funct., Genet. / Year: 1989
Title: Use of Restrained Molecular Dynamics in Water to Determine Three-Dimensional Protein Structure: Prediction of the Three-Dimensional Structure of Ecballium Elaterium Trypsin Inhibitor II
Authors: Chiche, L. / Gaboriaud, C. / Heitz, A. / Mornon, J.P. / Castro, B. / Kollman, P.A.
History
DepositionMar 12, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_sheet.number_strands
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: TRYPSIN
I: TRYPSIN INHIBITOR II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4363
Polymers27,3962
Non-polymers401
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-9.5 kcal/mol
Surface area11500 Å2
MethodPQS
Unit cell
Length a, b, c (Å)121.050, 121.050, 121.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein TRYPSIN


Mass: 23493.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / Secretion: SALIVA / References: UniProt: P00761, trypsin
#2: Protein/peptide TRYPSIN INHIBITOR II / EETI-II


Mass: 3902.500 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Details: C-TERMINAL TAG OF 6 HISTIDINES / Source: (synth.) ECBALLIUM ELATERIUM (jumping cucumber) / References: UniProt: P12071
#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


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION MET 7 ILE IN CHAIN I DUE TO RADIATION DAMAGE CYSTEINES WERE MODELLED PARTLY ...ENGINEERED MUTATION MET 7 ILE IN CHAIN I DUE TO RADIATION DAMAGE CYSTEINES WERE MODELLED PARTLY CLEAVED AND OXYDIZED TO SERINE
Has protein modificationY
Sequence detailsTHE MICROHETEROGENEITY FOR THE CYSTEINE/SERINES AT RESIDUES 22,42,58, 136, 157, 191, 201, 220 ...THE MICROHETEROGENEITY FOR THE CYSTEINE/SERINES AT RESIDUES 22,42,58, 136, 157, 191, 201, 220 (CHAIN E) AND RESIDUES 15, 27 (CHAIN I) ARE THE RESULT OF RADIATION DAMAGE DURING DATA COLLECTION THAT CAUSED THE REDUCTION OF THE DI-SUPHIDES AND OXIDATION OF THE CYS TO SER

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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: 2.7 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.7 / Details: pH 6.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 1999 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 49533 / % possible obs: 99.7 % / Redundancy: 8.05 % / Rmerge(I) obs: 0.0532 / Rsym value: 0.0278 / Net I/σ(I): 19.24
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.48 % / Rmerge(I) obs: 0.3755 / Mean I/σ(I) obs: 3.39 / Rsym value: 0.2779 / % possible all: 99.6

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LDT

1ldt


Resolution: 1.5→10 Å / Num. parameters: 8170 / Num. restraintsaints: 7778 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 2475 5 %RANDOM
all0.2349 49346 --
obs0.2331 -99.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 1746.9 / Occupancy sum non hydrogen: 1994.85
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 1 177 2065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0294
X-RAY DIFFRACTIONs_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.068
X-RAY DIFFRACTIONs_approx_iso_adps0

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