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- PDB-1h9i: COMPLEX OF EETI-II MUTANT WITH PORCINE TRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1h9i
TitleCOMPLEX OF EETI-II MUTANT WITH PORCINE TRYPSIN
Components
  • TRYPSIN
  • TRYPSIN INHIBITOR II
KeywordsHYDROLASE/INHIBITOR / COMPLEX (SERINE PROTEASE-INHIBITOR) / TRYPSIN / SQUASH INHIBITOR / CYSTINE KNOT / 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
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 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 1.6Oct 16, 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)27,5693
Polymers27,5292
Non-polymers401
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)139.862, 139.862, 33.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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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: 4035.668 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.: 135 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN I ENGINEERED MUTATIONS MET 7 ILE,GLY 22 THR,PRO 23 ASN AND GLY 25 LYS
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: 2.99 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.7 / Details: pH 6.70

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.54187
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 3, 2000 / Details: OSMIC MIRROR SYSTEM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 26024 / % possible obs: 99.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.0683 / Rsym value: 0.0405 / Net I/σ(I): 17.84
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.31 % / Rmerge(I) obs: 0.2171 / Mean I/σ(I) obs: 8.89 / Rsym value: 0.1031 / % possible all: 97.9

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Processing

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

1ldt


Resolution: 1.9→10 Å / Num. parameters: 8079 / Num. restraintsaints: 7813 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 1287 5 %RANDOM
all0.1423 25902 --
obs0.1416 -99.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 1741 / Occupancy sum non hydrogen: 1958
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 1 135 1969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0277
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.07
X-RAY DIFFRACTIONs_approx_iso_adps0

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