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- PDB-1g6x: ULTRA HIGH RESOLUTION STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHI... -

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Basic information

Entry
Database: PDB / ID: 1g6x
TitleULTRA HIGH RESOLUTION STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) MUTANT WITH ALTERED BINDING LOOP SEQUENCE
ComponentsPANCREATIC TRYPSIN INHIBITOR
KeywordsHYDROLASE INHIBITOR / SERINE PROTEASE INHIBITOR
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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...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 / 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 ...: / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / EXISTING MODEL / Resolution: 0.86 Å
AuthorsAddlagatta, A. / Czapinska, H. / Krzywda, S. / Otlewski, J. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Ultrahigh-resolution structure of a BPTI mutant.
Authors: Addlagatta, A. / Krzywda, S. / Czapinska, H. / Otlewski, J. / Jaskolski, M.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: High-Resolution Structure of Bovine Pancreatic Trypsin Inhibitor with Altered Binding Loop Sequenc
Authors: Czapinska, H. / Otlewski, J. / Krzywda, S. / Sheldrick, G.M. / Jaskolski, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of Bovine Pancreatic Trypsin Inhibitor at 125 K: Definition of Carboxyl-Terminal Residues Gly57 and Ala58
Authors: Parkin, S. / Rupp, B. / Hope, H.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Determination of a High Quality Nuclear Magnetic Resonance Solution Structure of the Bovine Pancreatic Trypsin Inhibitor and Comparison with Three Crystal Structures
Authors: Berndt, K. / Guentert, P. / Orbons, L.P. / Wuethrich, K.
#4: Journal: J.Mol.Biol. / Year: 1984
Title: Structure of Bovine Pancreatic Trypsin Inhibitor . Results of Joint Neutron and X-Ray Refinement of Crystal Form II
Authors: Wlodawer, A. / Walter, J. / Huber, R. / Sjolin, L.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1975
Title: Crystallographic Refinement of the Structure of Bovine Pancreatic Trypsin Inhibitor at 1.5 A Resolution
Authors: Deisenhofer, J. / Steigemann, W.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,37411
Polymers6,4811
Non-polymers89310
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: PANCREATIC TRYPSIN INHIBITOR
hetero molecules

A: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,74822
Polymers12,9632
Non-polymers1,78520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4390 Å2
ΔGint-182 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.891, 51.891, 43.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-64-

SO4

21A-65-

SO4

31A-121-

HOH

41A-133-

HOH

51A-164-

HOH

61A-203-

HOH

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Components

#1: Protein PANCREATIC TRYPSIN INHIBITOR / BPTI / APROTININ / TRASYLOL / BASIC PROTEASE INHIBITOR


Mass: 6481.481 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P00974
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG 400, 2 M AMMONIUM SULFATE, 0.1 M NA HEPES. A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/2 UL ...Details: 2% PEG 400, 2 M AMMONIUM SULFATE, 0.1 M NA HEPES. A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/2 UL DROPS OF THE PROTEIN SOLUTION WERE MIXED WITH 2 UL OF RESERVOIR SOLUTION CONTAINING 2% PEG 400, 2 M AMMONIUM SULFATE AND 0.1 M NA HEPES, PH 7.5. THE HANGING DROPLETS WERE EQUILIBRATED AT 19 DEG C THROUGH THE GAS PHASE WITH THE RESERVOIR. PRISMATIC CRYSTALS MEASURING UP TO 0.4 MM GREW WITHIN 12 HOURS. FOR LOW-TEMPERATURE DATA COLLECTION (100 K), THE CRYSTAL WAS CRYOPROTECTED IN THE RESERVOIR SOLUTION SUPPLEMENTED BY 30 % ETHYLENE GLYCOL., VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7 / Details: Czapinska, H., (2000) J.Mol.Biol., 295, 1237.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
22 %PEG4001reservoir
32.0 Mammonium sulfate1reservoir
40.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 7, 1999
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 0.86→20 Å / Num. obs: 47018 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 54.1
Reflection shellResolution: 0.86→0.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.61 / % possible all: 88.6
Reflection
*PLUS
Num. measured all: 814213
Reflection shell
*PLUS
% possible obs: 88.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: EXISTING MODEL
Starting model: 1QLQ

1qlq


Resolution: 0.86→10 Å / Num. parameters: 6499 / Num. restraintsaints: 7361 / Cross valid method: FREE R
StereochEM target val spec case: ETHYLENE GLYCOL (EDO) AND SULFATE (SO4) GEOMETRY BASED ON DATA FROM CSD
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT WITHOUT STEREOCHEMICAL RESTRAINTS ON ORDERED MAIN CHAIN. THE COMPLETE C-TERMINUS IS VISIBLE. IT FORMS A SALT-BRIDGE WITH THE N-TERMINUS. ARG 39 IS DISORDERED IN TWO ...Details: ANISOTROPIC REFINEMENT WITHOUT STEREOCHEMICAL RESTRAINTS ON ORDERED MAIN CHAIN. THE COMPLETE C-TERMINUS IS VISIBLE. IT FORMS A SALT-BRIDGE WITH THE N-TERMINUS. ARG 39 IS DISORDERED IN TWO CONFORMATIONS. IN ADDITION, IT IS ADJACENT TO CYS 38 OF THE DISORDERED 14-38 DISULFIDE AND IS PART OF A DISORDERED ARGININE CAGE. ALA 58 IS THE C-TERMINAL RESIDUE. IT IMMEDIATELY FOLLOWS THE DISORDERED GLY 56 - GLY 57 DOUBLET. THE CYS14-CYS38 DISULFIDE BRIDGE IS OBSERVED IN TWO DISTINCT CHIRALITIES (60 % RIGHT-HANDED, 40 % LEFT-HANDED). THE MAIN CHAIN OF THREE RESIDUES AND THE SIDE CHAINS OF 10 RESIDUES ARE MODELED IN TWO CONFORMATIONS. EIGHT SULFATE ANIONS (TWO WITH TWO-FOLD SYMMETRY) ARE PRESENT IN THE ASYMMETRIC UNIT. ONE OF THEM SHARES A SITE WITH THREE WATER MOLECULES. TWO ETHYLENE GLYCOL MOLECULES MODELED PER ONE PROTEIN MOLECULE. REFINEMENT CONCLUDED USING ONE CYCLE OF BLOCKED FULL-MATRIX LEAST-SQUARES ALGORITHM.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 1883 4 %RANDOM
all0.1072 46998 --
obs0.1068 -94.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 426 / Occupancy sum non hydrogen: 603
Refinement stepCycle: LAST / Resolution: 0.86→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 44 170 666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.023
X-RAY DIFFRACTIONs_angle_d0.043
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.035
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.081
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.094
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 4 % / Rfactor Rfree: 0.14 / Rfactor Rwork: 0.107
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.113

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