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- PDB-6f1f: The methylene thioacetal BPTI (Bovine Pancreatic Trypsin Inhibito... -

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Basic information

Entry
Database: PDB / ID: 6f1f
TitleThe methylene thioacetal BPTI (Bovine Pancreatic Trypsin Inhibitor) mutant structure
ComponentsPancreatic trypsin inhibitor
KeywordsBLOOD CLOTTING / Methylene thioacetal / Inhibitor / BPTI / methylenedithioether
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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
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 / Irregular
Similarity search - Domain/homology
Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.716 Å
AuthorsLansky, S. / Mousa, R. / Metanis, N. / Shoham, G.
CitationJournal: Chem Sci / Year: 2018
Title: BPTI folding revisited: switching a disulfide into methylene thioacetal reveals a previously hidden path.
Authors: Mousa, R. / Lansky, S. / Shoham, G. / Metanis, N.
History
DepositionNov 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pancreatic trypsin inhibitor
B: Pancreatic trypsin inhibitor
C: Pancreatic trypsin inhibitor
D: Pancreatic trypsin inhibitor
E: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,28632
Polymers32,7085
Non-polymers2,57827
Water3,999222
1
A: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1147
Polymers6,5421
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2108
Polymers6,5421
Non-polymers6687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1147
Polymers6,5421
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9265
Polymers6,5421
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9225
Polymers6,5421
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: Pancreatic trypsin inhibitor
B: Pancreatic trypsin inhibitor
C: Pancreatic trypsin inhibitor
D: Pancreatic trypsin inhibitor
E: Pancreatic trypsin inhibitor
hetero molecules

A: Pancreatic trypsin inhibitor
B: Pancreatic trypsin inhibitor
C: Pancreatic trypsin inhibitor
D: Pancreatic trypsin inhibitor
E: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,57264
Polymers65,41610
Non-polymers5,15654
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area25740 Å2
ΔGint-707 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.510, 95.510, 157.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-247-

HOH

21A-248-

HOH

31A-249-

HOH

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Components

#1: Protein
Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPTI


Mass: 6541.595 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P00974
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2M AmSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.716→47.77 Å / Num. obs: 45433 / % possible obs: 98.9 % / Redundancy: 40 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 34.98
Reflection shellResolution: 1.716→1.82 Å / Redundancy: 39.9 % / Rmerge(I) obs: 1.739 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 6781 / CC1/2: 0.89 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HEX

2hex


Resolution: 1.716→40.808 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.83
RfactorNum. reflection% reflection
Rfree0.2073 2258 4.99 %
Rwork0.1891 --
obs0.1901 45219 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.716→40.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 139 222 2606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112607
X-RAY DIFFRACTIONf_angle_d1.5483537
X-RAY DIFFRACTIONf_dihedral_angle_d16.142050
X-RAY DIFFRACTIONf_chiral_restr0.078315
X-RAY DIFFRACTIONf_plane_restr0.008444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7165-1.75380.47161090.46722061X-RAY DIFFRACTION77
1.7538-1.79460.3371410.31842671X-RAY DIFFRACTION100
1.7946-1.83950.29241400.25492670X-RAY DIFFRACTION100
1.8395-1.88920.25251390.23192658X-RAY DIFFRACTION100
1.8892-1.94480.28161420.22222681X-RAY DIFFRACTION100
1.9448-2.00760.23541380.21752660X-RAY DIFFRACTION100
2.0076-2.07930.27281430.20672702X-RAY DIFFRACTION100
2.0793-2.16260.25041410.21852678X-RAY DIFFRACTION100
2.1626-2.2610.28341400.21632695X-RAY DIFFRACTION100
2.261-2.38020.24071440.21142729X-RAY DIFFRACTION100
2.3802-2.52930.26431430.21232707X-RAY DIFFRACTION100
2.5293-2.72450.22981430.1952727X-RAY DIFFRACTION100
2.7245-2.99860.21641440.20022749X-RAY DIFFRACTION100
2.9986-3.43240.18181450.16932763X-RAY DIFFRACTION100
3.4324-4.32370.1611490.15282816X-RAY DIFFRACTION100
4.3237-40.81930.16661570.16982994X-RAY DIFFRACTION100

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