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- PDB-3auc: A simplified BPTI variant with poly SER (C5S) amino acid tag at t... -

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Basic information

Entry
Database: PDB / ID: 3auc
TitleA simplified BPTI variant with poly SER (C5S) amino acid tag 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 16, 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)13,4215
Polymers13,1332
Non-polymers2883
Water1,76598
1
A: Bovine pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)6,5661
Polymers6,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8554
Polymers6,5661
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.259, 48.391, 36.476
Angle α, β, γ (deg.)90.00, 108.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1122-

HOH

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Components

#1: Protein Bovine pancreatic trypsin inhibitor / BPTI


Mass: 6566.340 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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 98 / 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 SER 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.2M Lithium sulfate, 0.1M TrisHCl, 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 / Wavelength: 1 Å
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 wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→30.401 Å / Num. all: 8269 / Num. obs: 8269 / % possible obs: 96.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.227 / Rsym value: 0.213
Reflection shellResolution: 1.91→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.227 / Num. unique all: 8369 / % possible all: 96.2

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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: 1.91→30.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.119 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25039 360 4.6 %RANDOM
Rwork0.17843 ---
obs0.18165 7463 94.61 %-
all-8269 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.39 Å2
2--0.03 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.91→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 15 98 943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022868
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.9541181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.5821.05338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41515105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.265159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02693
X-RAY DIFFRACTIONr_nbd_refined0.1990.2422
X-RAY DIFFRACTIONr_nbtor_refined0.3250.2590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4330.28
X-RAY DIFFRACTIONr_mcbond_it1.6761.5572
X-RAY DIFFRACTIONr_mcangle_it2.4872874
X-RAY DIFFRACTIONr_scbond_it4.5233334
X-RAY DIFFRACTIONr_scangle_it6.144.5306
LS refinement shellResolution: 1.913→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 806 -
Rwork0.178 407 -
obs-8269 96.2 %

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