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- PDB-2xtt: Bovine trypsin in complex with evolutionary enhanced Schistocerca... -

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Basic information

Entry
Database: PDB / ID: 2xtt
TitleBovine trypsin in complex with evolutionary enhanced Schistocerca gregaria protease inhibitor 1 (SGPI-1-P02)
Components
  • CATIONIC TRYPSIN
  • PROTEASE INHIBITOR SGPI-1
KeywordsHYDROLASE / CATALYTIC MECHANISM / INHIBITION / IN VITRO EVOLUTION
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / : / 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 ...Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / : / 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
ACETATE ION / Serine protease inhibitor I/II / Serine protease 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
SCHISTOCERCA GREGARIA (desert locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsWahlgren, W.Y. / Pal, G. / Kardos, J. / Porrogi, P. / Szenthe, B. / Patthy, A. / Graf, L. / Katona, G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action.
Authors: Wahlgren, W.Y. / Pal, G. / Kardos, J. / Porrogi, P. / Szenthe, B. / Patthy, A. / Graf, L. / Katona, G.
History
DepositionOct 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.6Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 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 "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" 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
A: PROTEASE INHIBITOR SGPI-1
B: CATIONIC TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3564
Polymers27,2572
Non-polymers992
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-18.1 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.910, 63.610, 43.870
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide PROTEASE INHIBITOR SGPI-1 / PROTEASE INHIBITOR SGPI-1 / SCHISTOCERCA GREGARIA TRYPSIN INHIBITOR / PROTEASE INHIBITOR SGPI-2 / ...PROTEASE INHIBITOR SGPI-1 / SCHISTOCERCA GREGARIA TRYPSIN INHIBITOR / PROTEASE INHIBITOR SGPI-2 / SCHISTOCERCA GREGARIA CHYMOTRYPSIN INHIBITOR / SGTI / SGCI


Mass: 3932.404 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-54 / Source method: obtained synthetically / Details: IN VITRO EVOLVED SEQUENCE WITH THE FOLLOWING / Source: (synth.) SCHISTOCERCA GREGARIA (desert locust) / References: UniProt: O46162
#2: Protein CATIONIC TRYPSIN / BETA-TRYPSIN / ALPHA-TRYPSIN CHAIN 1 / ALPHA-TRYPSIN CHAIN 2


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Cell: ACINAR CELLS / Organ: PANCREAS / Tissue: GLANDULAR / References: UniProt: P00760, trypsin
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN VITRO EVOLVED SEQUENCE FOR CHAIN A.

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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: 1.89 Å3/Da / Density % sol: 34.9 % / Description: NONE
Crystal growpH: 4.6
Details: EQUAL AMOUNT OF PROTEIN SOLUTION (9.1 MG/ML PROTEIN COMPLEX IN 0.5 MM MES PH 6.0 BUFFER) AND PRECIPITANT SOLUTION (30% PEG 4000, 0.3 M AMMONIUM ACETATE, 0.1 M NA-ACETATE PH 4.6) WERE MIXED ...Details: EQUAL AMOUNT OF PROTEIN SOLUTION (9.1 MG/ML PROTEIN COMPLEX IN 0.5 MM MES PH 6.0 BUFFER) AND PRECIPITANT SOLUTION (30% PEG 4000, 0.3 M AMMONIUM ACETATE, 0.1 M NA-ACETATE PH 4.6) WERE MIXED AND EQUILIBRATED AGAINST 0.5 ML PRECIPITANT SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 0.93→43.8 Å / Num. obs: 135272 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.9
Reflection shellResolution: 0.93→0.98 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 54

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K1J

1k1j


Resolution: 0.93→10 Å / Num. parameters: 20959 / Num. restraintsaints: 25983 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: ASP-102, HIS-57, SER-195, ASP-194, GLY-193, SER-214 AND SCISSILE PEPTIDE BOND OF INHIBITOR
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.044. THE STRUCTURE WAS REFINED USING UNMERGED REFLECTIONS IN SHELX. THIS DATASET IS INCLUDED WITH THE MAIN STRUCTURE FACTOR FILE ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.044. THE STRUCTURE WAS REFINED USING UNMERGED REFLECTIONS IN SHELX. THIS DATASET IS INCLUDED WITH THE MAIN STRUCTURE FACTOR FILE R2XTTSF AS A SECOND DATASET.
RfactorNum. reflection% reflectionSelection details
Rfree0.1397 2035 1.6 %RANDOM
all0.1168 122128 --
obs--91 %-
Refine analyzeNum. disordered residues: 21 / Occupancy sum hydrogen: 1820.58 / Occupancy sum non hydrogen: 2225.9
Refinement stepCycle: LAST / Resolution: 0.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 5 350 2231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0346
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.107
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.121
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.116

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