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- PDB-3aui: A simplified BPTI variant with poly Glu amino acid tag (C3E) at t... -

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Basic information

Entry
Database: PDB / ID: 3aui
TitleA simplified BPTI variant with poly Glu amino acid tag (C3E) at the C-terminus
ComponentsBovine pancreatic trypsin inhibitor
KeywordsHYDROLASE INHIBITOR / Serine protease inhibitor / Inhibits serine protease / Trypsin
Function / homologyPancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Few Secondary Structures / Irregular
Function and homology information
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 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 on 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 ...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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1694
Polymers12,9772
Non-polymers1922
Water2,828157
1
A: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5842
Polymers6,4881
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5842
Polymers6,4881
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.849, 48.858, 36.790
Angle α, β, γ (deg.)90.00, 109.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-192-

HOH

21A-266-

HOH

31B-273-

HOH

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Components

#1: Protein Bovine pancreatic trypsin inhibitor / BPTI


Mass: 6488.268 Da / Num. of mol.: 2 / Mutation: A1014G, A1038V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): JM109(DE3)PLYSS / Cellular location (production host): Inclusion body / Production host: Escherichia Coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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. THREE GLU RESIDUE TAG AT THE C-TERMINUS.

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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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 25% PEG4000, 0.2M Lithium sulfate, 0.1M sodium acetate, pH 4.7, 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: Oct 25, 2010
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.851→38.208 Å / Num. all: 9357 / Num. obs: 9351 / % possible obs: 92.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.23
Reflection shellResolution: 1.851→1.9 Å / % possible all: 92.6

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Processing

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

4pti


Resolution: 1.851→38.208 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.805 / SU B: 4.251 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31202 425 4.7 %RANDOM
Rwork0.22317 ---
all0.2282 9357 --
obs0.22706 8526 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.919 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.03 Å2
2--1.2 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.851→38.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 10 157 1006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022896
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9461221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.7752040
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3515112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5381512
X-RAY DIFFRACTIONr_chiral_restr0.1240.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02728
X-RAY DIFFRACTIONr_nbd_refined0.2260.2461
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.214
X-RAY DIFFRACTIONr_mcbond_it0.9671.5593
X-RAY DIFFRACTIONr_mcangle_it1.3782900
X-RAY DIFFRACTIONr_scbond_it2.2853347
X-RAY DIFFRACTIONr_scangle_it2.9854.5317
LS refinement shellResolution: 1.851→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.77 20 -
Rwork0.322 373 -
obs--58.48 %

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