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- PDB-3aud: Simplified BPTI variant with poly Asn amino acid tag (C5N) at the... -

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Basic information

Entry
Database: PDB / ID: 3aud
TitleSimplified BPTI variant with poly Asn amino acid tag (C5N) at the C-terminus
ComponentsBovine pancreatic trypsin inhibitorAprotinin
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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.943 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 / 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
C: Bovine pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)20,1043
Polymers20,1043
Non-polymers00
Water3,207178
1
A: Bovine pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)6,7011
Polymers6,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bovine pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)6,7011
Polymers6,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bovine pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)6,7011
Polymers6,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Bovine pancreatic trypsin inhibitor
B: Bovine pancreatic trypsin inhibitor
C: Bovine pancreatic trypsin inhibitor

A: Bovine pancreatic trypsin inhibitor
B: Bovine pancreatic trypsin inhibitor
C: Bovine pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)40,2096
Polymers40,2096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area7210 Å2
ΔGint-30 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.485, 61.485, 171.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-177-

HOH

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Components

#1: Protein Bovine pancreatic trypsin inhibitor / Aprotinin / BPTI


Mass: 6701.467 Da / Num. of mol.: 3 / Mutation: A1014G, A1038V
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 / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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. FIVE ASN 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.0M Sodium Formate, 15mM TrisHCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2008
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.943→45.268 Å / Num. all: 14990 / Num. obs: 14990 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 20.4 % / Rmerge(I) obs: 0.368
Reflection shellResolution: 1.943→2.02 Å / Rmerge(I) obs: 0.368 / % possible all: 99.9

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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: 1.943→45.268 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.737 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19381 757 5.1 %RANDOM
Rwork0.15586 ---
obs0.15773 14213 99.87 %-
all-14990 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.918 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.943→45.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 0 178 1424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221305
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9391775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1720.16959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54615165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2321517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021061
X-RAY DIFFRACTIONr_nbd_refined0.1920.2613
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4630.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4960.232
X-RAY DIFFRACTIONr_mcbond_it1.1281.5861
X-RAY DIFFRACTIONr_mcangle_it1.7621319
X-RAY DIFFRACTIONr_scbond_it3.2173506
X-RAY DIFFRACTIONr_scangle_it4.6344.5453
LS refinement shellResolution: 1.943→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 53 -
Rwork0.152 1000 -
obs--98.69 %

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