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- PDB-1b0c: EVIDENCE OF A COMMON DECAMER IN THREE CRYSTAL STRUCTURES OF BPTI,... -

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Basic information

Entry
Database: PDB / ID: 1b0c
TitleEVIDENCE OF A COMMON DECAMER IN THREE CRYSTAL STRUCTURES OF BPTI, CRYSTALLIZED FROM THIOCYANATE, CHLORIDE OR SULFATE
ComponentsPROTEIN (PANCREATIC 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 / 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: 2.8 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 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)


Theoretical massNumber of molelcules
Total (without water)32,6385
Polymers32,6385
Non-polymers00
Water1,04558
1
A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)

A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)


Theoretical massNumber of molelcules
Total (without water)65,27610
Polymers65,27610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)95.470, 95.470, 159.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.936918, -0.279679, -0.209678), (0.292717, 0.299889, 0.907956), (-0.191056, -0.912056, 0.362838)26.8161, -46.825, 84.2046
2given(0.844053, -0.179696, -0.505257), (0.167754, -0.806422, 0.567047), (-0.509346, -0.563377, -0.650518)46.8711, 20.9744, 152.3607
3given(0.839134, 0.175766, -0.514743), (-0.171677, -0.812391, -0.557269), (-0.516121, 0.555992, -0.65153)34.6748, 110.901, 111.4845
4given(0.939976, 0.277804, -0.198169), (-0.282692, 0.308661, -0.908193), (-0.191132, 0.9097, 0.368667)5.5089, 97.8479, 16.9573

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Components

#1: Protein
PROTEIN (PANCREATIC TRYPSIN INHIBITOR) / BASIC PROTEASE INHIBITOR / BPI / BPTI / APROTININ


Mass: 6527.568 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.23 Å3/Da / Density % sol: 61 %
Crystal growpH: 4.5
Details: ACETATE BUFFER PH=4.5 BPTI 60 TO 100 MG/ML NACL 1.6 TO 2 M
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium acetate1reservoir
260-100 mg/mlinhibitor1drop
31.6-2 M1dropNaCl

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 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: 2.8→18 Å / Num. obs: 11127 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 55.8 Å2 / Rsym value: 0.038 / Net I/σ(I): 17.2
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.14 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.77 Å / % possible obs: 89.3 % / Num. measured all: 107368 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 2.77 Å / Lowest resolution: 2.84 Å / % possible obs: 55.5 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Agrovatadata reduction
ROTAVATAdata reduction
AMoREphasing
X-PLOR3.851refinement
Agrovatadata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PTI

6pti


Resolution: 2.8→18 Å / Rfactor Rfree error: 0.007 / 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
Rfree0.223 1125 10.3 %RANDOM
Rwork0.198 ---
obs0.198 10908 98 %-
Displacement parametersBiso mean: 37.1 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: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 0 58 2186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
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
11CONSTRX-RAY DIFFRACTION0.0294300
22X-RAY DIFFRACTION0.0266300
33X-RAY DIFFRACTION0.0286300
44X-RAY DIFFRACTION0.0258300
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.348 108 10.2 %
Rwork0.3 950 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.3

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