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- PDB-1bz5: EVIDENCE OF A COMMON DECAMER IN THREE CRYSTAL STRUCTURES OF BPTI,... -

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Basic information

Entry
Database: PDB / ID: 1bz5
TitleEVIDENCE OF A COMMON DECAMER IN THREE CRYSTAL STRUCTURES OF BPTI, CRYSTALLIZE FROM THIOCYANATE, CHLORIDE OR SULFATE
ComponentsPANCREATIC TRYPSIN INHIBITOR
KeywordsHYDROLASE INHIBITOR / BOVINE PANCREATIC TRYPSIN INHIBITOR / PENTAMERIC MOLECULE
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 / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsHamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A. / Lafont, S. / Astier, J.P. / Veesler, S.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The BPTI decamer observed in acidic pH crystal forms pre-exists as a stable species in solution.
Authors: Hamiaux, C. / Perez, J. / Prange, T. / Veesler, S. / Ries-Kautt, M. / Vachette, P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The Decameric Structure of Bovine Pancreatic Trypsin Inhibitor (BPTI) Crystallized from Thiocyanate at 2.7A Resolution
Authors: Hamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A. / Lafont, S. / Astier, J.P. / Veesler, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Decamers Observed in the Crystals of Bovine Panreatic Trypsin Inhibitor
Authors: Lubkowski, J. / Wlodawer, A.
History
DepositionNov 5, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)32,9268
Polymers32,6385
Non-polymers2883
Water1,982110
1
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)65,85216
Polymers65,27610
Non-polymers5766
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area16800 Å2
ΔGint-202 kcal/mol
Surface area22720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.480, 120.480, 111.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-202-

SO4

21D-225-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.549817, -0.83449, 0.036434), (0.539182, 0.387887, 0.747547), (-0.637953, -0.391369, 0.663209)55.4599, -25.9655, 58.8471
2given(-0.141528, -0.807289, -0.572935), (0.056301, -0.584388, 0.809519), (-0.988332, 0.082313, 0.128159)109.0064, 36.7028, 74.1603
3given(-0.164227, 0.037002, -0.985728), (-0.792082, -0.600527, 0.109422), (-0.587908, 0.798748, 0.127932)88.2759, 102.3032, 24.4843
4given(0.557274, 0.534833, -0.635137), (-0.829861, 0.384425, -0.404411), (0.02787, 0.752443, 0.658068)20.6503, 80.087, -21.4592

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Components

#1: Protein
PANCREATIC TRYPSIN INHIBITOR


Mass: 6527.568 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00974
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.58 Å3/Da / Density % sol: 65.55 %
Crystal growpH: 4.5
Details: SODIUM ACETATE BUFFER,PH=4.5 AMMONIUM SULPHATE 1.7 - 1.9M BPTI 10 - 20 MG/ML
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMsodium acetate1reservoir
210 mg/mlinhibitor1drop
31.8 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.58→19.8 Å / Num. obs: 15263 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 8.6 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.037 / Net I/σ(I): 20.7
Reflection shellResolution: 2.58→2.67 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.146 / % possible all: 91.1
Reflection
*PLUS
Num. measured all: 131366 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 91.1 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PTI

6pti


Resolution: 2.58→19.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1545 10.1 %RANDOM
Rwork0.19 ---
obs0.19 15239 98.3 %-
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.58→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 15 110 2317
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.07
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
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTX-RAY DIFFRACTION0.0223300
22X-RAY DIFFRACTION0.0169300
33X-RAY DIFFRACTION0.0219300
44X-RAY DIFFRACTION0.0209300
LS refinement shellResolution: 2.58→2.67 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 136 10.1 %
Rwork0.299 1211 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3SO4.PARSO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.07
LS refinement shell
*PLUS
Rfactor Rfree: 0.306 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.299

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