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- PDB-3aub: A simplified BPTI variant stabilized by the A14G and A38V substit... -

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Basic information

Entry
Database: PDB / ID: 3aub
TitleA simplified BPTI variant stabilized by the A14G and A38V substitutions
ComponentsBovine Pancreatic trypsin inhibitor
KeywordsHYDROLASE INHIBITOR / Serine protease inhibitor / Trypsin
Function / homologyPancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Few Secondary Structures / Irregular
Function and homology information
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsIslam, M.M. / Kato, A. / Khan, M.M.A. / Noguchi, K. / Yohda, M. / Kidokoro, S.I. / Kuroda, Y.
CitationJournal: To be Published
Title: Effect of amino acid mutations of protein's solubility, function and structure characterized using short poly amino acid peptide tags
Authors: Islam, M.M. / Kato, A. / Khan, M.M.A. / Noguchi, K. / Yohda, M. / Kidokoro, S.I. / Kuroda, Y.
History
DepositionFeb 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Assembly

Deposited unit
A: Bovine Pancreatic trypsin inhibitor
B: Bovine Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)11,9742
Polymers11,9742
Non-polymers00
Water4,558253
1
A: Bovine Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)5,9871
Polymers5,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bovine Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)5,9871
Polymers5,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.333, 39.058, 49.231
Angle α, β, γ (deg.)90.00, 101.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-161-

HOH

21B-235-

HOH

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Components

#1: Protein Bovine Pancreatic trypsin inhibitor / BPTI


Mass: 5986.823 Da / Num. of mol.: 2 / Mutation: A14G, A38V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): JM109(DE3)PLYSS / Cellular location (production host): Inclusion body / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS A SIMPLIFIED BPTI VARIANT WITH 21 ALANINES, AND IT HAS BEEN STABILIZED WITH THE ...THIS SEQUENCE IS A SIMPLIFIED BPTI VARIANT WITH 21 ALANINES, AND IT HAS BEEN STABILIZED WITH THE A14G AND A38V MUTATIONS.

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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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG4000 ,15% Iisopropanol, 0.1M Sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 22, 2006
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→48.224 Å / Num. all: 53613 / Num. obs: 53613 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.294 / Rsym value: 0.243
Reflection shellResolution: 1→1.04 Å / Redundancy: 4 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 0.243 / Num. unique all: 53613 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
Cootmodel building
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PTI

4pti


Resolution: 1→48.22 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.672 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17931 2624 5.1 %RANDOM
Rwork0.16591 ---
obs0.16659 49180 96.63 %-
all-53613 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.2 Å2
2--0.02 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms842 0 0 253 1095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022937
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.941286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.28820.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00815117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1421511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02787
X-RAY DIFFRACTIONr_nbd_refined0.1890.2485
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0870.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.247
X-RAY DIFFRACTIONr_mcbond_it0.5951.5613
X-RAY DIFFRACTIONr_mcangle_it0.9042938
X-RAY DIFFRACTIONr_scbond_it1.3983376
X-RAY DIFFRACTIONr_scangle_it1.6384.5340
X-RAY DIFFRACTIONr_rigid_bond_restr1.0093989
X-RAY DIFFRACTIONr_sphericity_free1.773253
X-RAY DIFFRACTIONr_sphericity_bonded1.9443902
LS refinement shellResolution: 1→1.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1793 4433 -
Rwork0.1659 3046 -
obs-53613 96.6 %

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