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- PDB-4y0z: Trypsin in complex with with BPTI mutant AMINOBUTYRIC ACID -

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Basic information

Entry
Database: PDB / ID: 4y0z
TitleTrypsin in complex with with BPTI mutant AMINOBUTYRIC ACID
Components
  • Cationic trypsin
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR COMPLEX / HYDROLASE INHIBITORS / METAL-BINDING / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX complex
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / endopeptidase activity / protease binding / 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 / Few Secondary Structures ...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 domain profile. / Serine proteases, trypsin family, serine active site. / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsLoll, B. / Ye, S. / Berger, A.A. / Muelow, U. / Alings, C. / Wahl, M.C. / Koksch, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGraduate 25 School GRK 1582/1 Germany
CitationJournal: Chem Sci / Year: 2015
Title: Fluorine teams up with water to restore inhibitor activity to mutant BPTI.
Authors: Ye, S. / Loll, B. / Berger, A.A. / Mulow, U. / Alings, C. / Wahl, M.C. / Koksch, B.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 2.0Apr 18, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.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)30,99315
Polymers29,8082
Non-polymers1,18513
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-141 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.907, 82.299, 123.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules EI

#1: Protein Cationic trypsin / Beta-trypsin / trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPTI


Mass: 6483.493 Da / Num. of mol.: 1 / Fragment: UNP residues 36-93 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) Bos taurus (cattle) / References: UniProt: P00974

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Non-polymers , 4 types, 381 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 1.8 to 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 3, 2013
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 79301 / % possible obs: 98.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.4
Reflection shellResolution: 1.37→1.45 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.9 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→34.23 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1563 3964 5 %Random selection
Rwork0.1335 ---
obs0.1346 79296 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 63 368 2500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142371
X-RAY DIFFRACTIONf_angle_d1.4233240
X-RAY DIFFRACTIONf_dihedral_angle_d11.289882
X-RAY DIFFRACTIONf_chiral_restr0.087353
X-RAY DIFFRACTIONf_plane_restr0.009414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3674-1.38410.30021250.26662388X-RAY DIFFRACTION88
1.3841-1.40160.27041400.23672656X-RAY DIFFRACTION98
1.4016-1.420.26711370.22652600X-RAY DIFFRACTION98
1.42-1.43950.24641400.20392658X-RAY DIFFRACTION98
1.4395-1.460.20131410.18482683X-RAY DIFFRACTION98
1.46-1.48180.20781400.17552656X-RAY DIFFRACTION98
1.4818-1.5050.21331400.16932659X-RAY DIFFRACTION98
1.505-1.52970.21390.16522639X-RAY DIFFRACTION98
1.5297-1.5560.2061400.15662662X-RAY DIFFRACTION99
1.556-1.58430.1561420.13992702X-RAY DIFFRACTION99
1.5843-1.61480.16681400.1332655X-RAY DIFFRACTION99
1.6148-1.64780.171410.12312689X-RAY DIFFRACTION99
1.6478-1.68360.15271420.11762690X-RAY DIFFRACTION99
1.6836-1.72280.14921410.11642687X-RAY DIFFRACTION99
1.7228-1.76580.14641430.12122704X-RAY DIFFRACTION99
1.7658-1.81360.16551400.11862665X-RAY DIFFRACTION99
1.8136-1.8670.14431420.11552710X-RAY DIFFRACTION99
1.867-1.92720.14421430.11392704X-RAY DIFFRACTION99
1.9272-1.99610.1421410.11332690X-RAY DIFFRACTION99
1.9961-2.0760.12671450.11222754X-RAY DIFFRACTION99
2.076-2.17050.12941430.11332707X-RAY DIFFRACTION100
2.1705-2.28490.13111430.1142724X-RAY DIFFRACTION99
2.2849-2.4280.14531440.12122736X-RAY DIFFRACTION100
2.428-2.61540.1421440.12772731X-RAY DIFFRACTION100
2.6154-2.87850.16281460.13712773X-RAY DIFFRACTION100
2.8785-3.29470.15991460.13512778X-RAY DIFFRACTION100
3.2947-4.14980.14451470.11782798X-RAY DIFFRACTION100
4.1498-34.24090.1581490.15842834X-RAY DIFFRACTION97

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