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- PDB-3otj: A Crystal Structure of Trypsin Complexed with BPTI (Bovine Pancre... -

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Basic information

Entry
Database: PDB / ID: 3otj
TitleA Crystal Structure of Trypsin Complexed with BPTI (Bovine Pancreatic Trypsin Inhibitor) by X-ray/Neutron Joint Refinement
Components
  • Cationic trypsin
  • Pancreatic trypsin inhibitor
KeywordsHydrolase/Hydrolase Inhibitor / Complex / Hydrolase / Inhibitor / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / : / Few Secondary Structures / Irregular / 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
DEUTERATED WATER / Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / Resolution: 2.15 Å
AuthorsKawamura, K. / Yamada, T. / Kurihara, K. / Tamada, T. / Kuroki, R. / Tanaka, I. / Takahashi, H. / Niimura, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: X-ray and neutron protein crystallographic analysis of the trypsin-BPTI complex.
Authors: Kawamura, K. / Yamada, T. / Kurihara, K. / Tamada, T. / Kuroki, R. / Tanaka, I. / Takahashi, H. / Niimura, N.
History
DepositionSep 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Data collection
Revision 1.3Aug 21, 2011Group: Other
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3728
Polymers29,8522
Non-polymers5206
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.604, 85.361, 122.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Description: Purchased / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin
#2: Protein Pancreatic trypsin inhibitor / Basic protease inhibitor / BPTI / BPI / Aprotinin


Mass: 6527.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Description: Purchased / Production host: Escherichia coli (E. coli) / References: UniProt: P00974
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 298 K / pH: 7.5
Details: (NH4)2SO4, CaCl2, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength
NUCLEAR REACTOR12.6
SYNCHROTRONPhoton Factory BL-6A21
Detector
TypeIDDetectorDate
NEUTRON IMAGING PLATE1IMAGE PLATENov 21, 2008
ADSC QUANTUM 4r2CCDJun 13, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1ELASTICALLY-BENT PERFECT SI(111)SINGLE WAVELENGTHMneutron1
2TRIANGULAR SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.61
211
ReflectionResolution: 2.15→37.89 Å / Num. obs: 20552 / % possible obs: 92.7 % / Rmerge(I) obs: 0.144
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 0.387 / % possible all: 90.9

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Processing

Software
NameClassification
nCNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
nCNSphasing
Refinement

R Free selection details: RANDOM

Resolution (Å)Refine-IDBiso mean (Å2)Baniso 11 (Å2)Baniso 12 (Å2)Baniso 13 (Å2)Baniso 22 (Å2)Baniso 23 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection Rfree (%)Diffraction-IDσ(F)Stereochemistry target valuesBsol (Å2)ksol (e/Å3)Details% reflection obs (%)Cross valid method
2.15-37.89NEUTRON DIFFRACTION24.262.3800-2.320-0.590.2260.20910382194920345510JOINT MAXIMUM LIKELIHOOD TARGET20.0530.6322An H nucleus is expressed as a D nucleus with a negetive occupancy factor of -0.56 (i.e. -0.375/0.667).
1.6-35.94X-RAY DIFFRACTION2.5500-5.3902.840.2090.1982630521695242.25420.37833299THROUGHOUT
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.280.25
Luzzati d res low-5
Luzzati sigma a0.30.29
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.20.19
Luzzati d res low-5
Luzzati sigma a0.120.12
Refinement stepCycle: LAST / Resolution: 2.15→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 26 120 2229
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.013
NEUTRON DIFFRACTIONc_dihedral_angle_d15.65
NEUTRON DIFFRACTIONc_improper_angle_d21.07
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shell

Total num. of bins used: 20 / % reflection Rfree: 4 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID
2.15-2.190.283480.304947NEUTRON DIFFRACTION
1.6-1.630.2611030.2452461X-RAY DIFFRACTION

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