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- PDB-3btd: The Crystal Structures of the Complexes Between the Bovine Beta-T... -

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Basic information

Entry
Database: PDB / ID: 3btd
TitleThe Crystal Structures of the Complexes Between the Bovine Beta-Trypsin and Ten P1 Variants of BPTI.
Components
  • PROTEIN (BOVINE PANCREATIC TRYPSIN INHIBITOR)
  • PROTEIN (TRYPSIN)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TRYPSIN / BPTI / SERINE PROTEINASE / 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 / 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
Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHelland, R. / Otlewski, J. / Sundheim, O. / Dadlez, M. / Smalas, A.O.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: The crystal structures of the complexes between bovine beta-trypsin and ten P1 variants of BPTI.
Authors: Helland, R. / Otlewski, J. / Sundheim, O. / Dadlez, M. / Smalas, A.O.
History
DepositionMar 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PROTEIN (TRYPSIN)
I: PROTEIN (BOVINE PANCREATIC TRYPSIN INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2447
Polymers29,8202
Non-polymers4245
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-66 kcal/mol
Surface area11120 Å2
MethodPISA
2
E: PROTEIN (TRYPSIN)
I: PROTEIN (BOVINE PANCREATIC TRYPSIN INHIBITOR)
hetero molecules

E: PROTEIN (TRYPSIN)
I: PROTEIN (BOVINE PANCREATIC TRYPSIN INHIBITOR)
hetero molecules

E: PROTEIN (TRYPSIN)
I: PROTEIN (BOVINE PANCREATIC TRYPSIN INHIBITOR)
hetero molecules

E: PROTEIN (TRYPSIN)
I: PROTEIN (BOVINE PANCREATIC TRYPSIN INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,97628
Polymers119,2798
Non-polymers1,69720
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area15940 Å2
ΔGint-325 kcal/mol
Surface area37210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.630, 84.770, 122.940
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 PROTEIN (TRYPSIN)


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Protein PROTEIN (BOVINE PANCREATIC TRYPSIN INHIBITOR)


Mass: 6495.438 Da / Num. of mol.: 1 / Mutation: K15D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Compound detailsP1 RESIDUE OF THE INHIBITOR IS MUTATED TO ASP
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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127 mg/mlprotein1drop
248-50 %satammonium sulfate1reservoir
30.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 31159 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 6.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.31 / % possible all: 99.5
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
X-PLORmodel building
X-PLOR3.8refinement
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PTC

2ptc


Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
Details: ENERGY TERMS OF THE INHIBITOR PEPTIDE SCISSILE BOND WERE SET TO ZERO DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.23 -10 %RANDOM
Rwork0.195 ---
obs-30633 98.8 %-
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 21 141 2169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→2 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.29 / Total num. of bins used: 8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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