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- PDB-4aoq: Cationic trypsin in complex with mutated Spinacia oleracea trypsi... -

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Basic information

Entry
Database: PDB / ID: 4aoq
TitleCationic trypsin in complex with mutated Spinacia oleracea trypsin inhibitor III (SOTI-III) (F14A)
Components
  • CATIONIC TRYPSIN
  • TRYPSIN INHIBITOR 3
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / MINIPROTEIN SCAFFOLD / KNOTTINS / SERINE PROTEASE INHIBITOR
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 / metal ion binding
Similarity search - Function
Trypsin inhibitor / Trypsin inhibitors 1,2 and 3 / : / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease ...Trypsin inhibitor / Trypsin inhibitors 1,2 and 3 / : / 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 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
Serine protease 1 / Trypsin inhibitor 3
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
SPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchmelz, S. / Glotzbach, B. / Reinwarth, M. / Christmann, A. / Kolmar, H. / Heinz, D.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Characterization of Spinacia Oleracea Trypsin Inhibitor III (Soti-III)
Authors: Glotzbach, B. / Schmelz, S. / Reinwarth, M. / Christmann, A. / Heinz, D.W. / Kolmar, H.
History
DepositionMar 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 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_site
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_asym_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_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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 "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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. THE SHEETS PRESENTED AS "BB" 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. THE SHEETS PRESENTED AS "CB" 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

Downloads & links

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Assembly

Deposited unit
A: CATIONIC TRYPSIN
B: CATIONIC TRYPSIN
C: CATIONIC TRYPSIN
D: TRYPSIN INHIBITOR 3
E: TRYPSIN INHIBITOR 3
F: TRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,62410
Polymers81,2666
Non-polymers3594
Water11,818656
1
A: CATIONIC TRYPSIN
D: TRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1293
Polymers27,0892
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-21.6 kcal/mol
Surface area10170 Å2
MethodPISA
2
B: CATIONIC TRYPSIN
E: TRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3674
Polymers27,0892
Non-polymers2782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-23.4 kcal/mol
Surface area10200 Å2
MethodPISA
3
C: CATIONIC TRYPSIN
F: TRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1293
Polymers27,0892
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-20.9 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.510, 68.380, 109.790
Angle α, β, γ (deg.)90.00, 93.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CATIONIC TRYPSIN / BETA-TRYPSIN / ALPHA-TRYPSIN CHAIN 1 / ALPHA-TRYPSIN CHAIN 2


Mass: 23324.287 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: SIGMA ALDRICH (T1426) / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide TRYPSIN INHIBITOR 3 / SOTI-III_F14A / SOTI III / TRYPSIN INHIBITOR III


Mass: 3764.358 Da / Num. of mol.: 3 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SPINACIA OLERACEA (spinach) / References: UniProt: P84781
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN D, PHE 12 TO ALA ENGINEERED RESIDUE IN CHAIN E, PHE 12 TO ALA ...ENGINEERED RESIDUE IN CHAIN D, PHE 12 TO ALA ENGINEERED RESIDUE IN CHAIN E, PHE 12 TO ALA ENGINEERED RESIDUE IN CHAIN F, PHE 12 TO ALA
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: 2.02 Å3/Da / Density % sol: 39.11 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL ...Details: TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL VOLUMES OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III F14A (1.5MM) AND PRECIPITANT SOLUTION (0.1M BICINE PH 9, 20% (W/V) PEG 6000) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 48020 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 10.57 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XTT

2xtt


Resolution: 2→19.889 Å / SU ML: 0.52 / σ(F): 1.99 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 2405 5 %
Rwork0.1667 --
obs0.1694 48006 98.82 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.539 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.845 Å20 Å2-0.9015 Å2
2---1.7329 Å20 Å2
3----2.1121 Å2
Refinement stepCycle: LAST / Resolution: 2→19.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5601 0 19 656 6276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046035
X-RAY DIFFRACTIONf_angle_d0.8628191
X-RAY DIFFRACTIONf_dihedral_angle_d14.0152174
X-RAY DIFFRACTIONf_chiral_restr0.06910
X-RAY DIFFRACTIONf_plane_restr0.0031079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04080.29471390.20592659X-RAY DIFFRACTION98
2.0408-2.08510.24221460.19462646X-RAY DIFFRACTION99
2.0851-2.13360.28551360.17812651X-RAY DIFFRACTION99
2.1336-2.18690.25031360.17622671X-RAY DIFFRACTION99
2.1869-2.24590.2391450.1752632X-RAY DIFFRACTION98
2.2459-2.31190.21931440.17772712X-RAY DIFFRACTION99
2.3119-2.38640.23261530.16572628X-RAY DIFFRACTION99
2.3864-2.47160.21571350.17222708X-RAY DIFFRACTION99
2.4716-2.57030.24521360.16732658X-RAY DIFFRACTION99
2.5703-2.6870.25191380.1732696X-RAY DIFFRACTION99
2.687-2.82830.24711520.17752670X-RAY DIFFRACTION99
2.8283-3.0050.22551270.17772698X-RAY DIFFRACTION99
3.005-3.23610.19281570.17182710X-RAY DIFFRACTION99
3.2361-3.56010.21571350.16952663X-RAY DIFFRACTION99
3.5601-4.07140.18341420.14742727X-RAY DIFFRACTION99
4.0714-5.1150.16531360.12752708X-RAY DIFFRACTION99
5.115-19.89010.19921480.15452764X-RAY DIFFRACTION99

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