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- PDB-3aue: A simplified BPTI variant with poly His amino acid tag (C5H) at t... -

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Basic information

Entry
Database: PDB / ID: 3aue
TitleA simplified BPTI variant with poly His amino acid tag (C5H) 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: 2.28 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
C: Bovine pancreatic trypsin inhibitor
D: Bovine pancreatic trypsin inhibitor
E: Bovine pancreatic trypsin inhibitor
F: Bovine pancreatic trypsin inhibitor
G: Bovine pancreatic trypsin inhibitor
H: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,58221
Polymers54,3338
Non-polymers1,24913
Water5,909328
1
A: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8882
Polymers6,7921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0804
Polymers6,7921
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9843
Polymers6,7921
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9843
Polymers6,7921
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9843
Polymers6,7921
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8882
Polymers6,7921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8882
Polymers6,7921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8882
Polymers6,7921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.011, 120.328, 53.322
Angle α, β, γ (deg.)90.00, 106.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bovine pancreatic trypsin inhibitor / BPTI


Mass: 6791.661 Da / Num. of mol.: 8 / 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.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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. FIVE HIS 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.2M Lithium sulfate, 0.1M Tris-HCl, pH 8.5, 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
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2009
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.28→38.954 Å / Num. all: 21392 / Num. obs: 21392 / % possible obs: 77.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.225
Reflection shellResolution: 2.28→2.38 Å / % possible all: 77.7

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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: 2.28→38.95 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.56 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 824 5 %RANDOM
Rwork0.16264 ---
obs0.16867 15499 76.3 %-
all-21392 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.17 Å2
2--0.16 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.28→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 65 328 3919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223696
X-RAY DIFFRACTIONr_angle_refined_deg2.1841.9395020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4665477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.98820.422166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44615432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9971541
X-RAY DIFFRACTIONr_chiral_restr0.1380.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022987
X-RAY DIFFRACTIONr_nbd_refined0.2270.21717
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.2287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5770.239
X-RAY DIFFRACTIONr_mcbond_it1.6951.52438
X-RAY DIFFRACTIONr_mcangle_it2.67923676
X-RAY DIFFRACTIONr_scbond_it4.40931444
X-RAY DIFFRACTIONr_scangle_it5.9894.51343
LS refinement shellResolution: 2.284→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 25 -
Rwork0.195 682 -
obs-21392 44.95 %

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