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- PDB-2zsc: Tamavidin2, Novel Avidin-like Biotin-Binding Proteins from an Edi... -

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Basic information

Entry
Database: PDB / ID: 2zsc
TitleTamavidin2, Novel Avidin-like Biotin-Binding Proteins from an Edible Mushroom
ComponentsTamavidin2
KeywordsBiotin Binding Protein / Avidin-like structure
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPleurotus cornucopiae (cornucopia mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKakuta, Y. / Okino, N. / Ito, M. / Yamamoto, T. / Takakura, Y.
CitationJournal: Febs J. / Year: 2009
Title: Tamavidins--novel avidin-like biotin-binding proteins from the Tamogitake mushroom
Authors: Takakura, Y. / Tsunashima, M. / Suzuki, J. / Usami, S. / Kakuta, Y. / Okino, N. / Ito, M. / Yamamoto, T.
History
DepositionSep 5, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tamavidin2
B: Tamavidin2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,35316
Polymers30,9622
Non-polymers1,39014
Water8,107450
1
A: Tamavidin2
B: Tamavidin2
hetero molecules

A: Tamavidin2
B: Tamavidin2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,70632
Polymers61,9254
Non-polymers2,78128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17270 Å2
ΔGint-70 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.382, 80.017, 55.733
Angle α, β, γ (deg.)90.00, 132.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tamavidin2


Mass: 15481.202 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus cornucopiae (cornucopia mushroom)
Description: Synonym is Tamogitake mushroom. / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B9A0T7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.2M MgCl2, 0.1M Bis-Tris pH 5.5, 0.1M NaCl, 0.025M MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 61099 / Num. obs: 61099 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 2
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1 / Num. unique all: 6217 / Rsym value: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SLG

1slg


Resolution: 1.3→18.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.794 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.073 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23758 3072 5.1 %RANDOM
Rwork0.19943 ---
obs0.20136 57683 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.472 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.05 Å2
2---0.09 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.3→18.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 89 450 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222235
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9713103
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45525.34986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.475155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021699
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.21280
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21503
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0050.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2193
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.292
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8371.51367
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30122224
X-RAY DIFFRACTIONr_scbond_it1.61431007
X-RAY DIFFRACTIONr_scangle_it2.2184.5838
X-RAY DIFFRACTIONr_rigid_bond_restr0.97532374
X-RAY DIFFRACTIONr_sphericity_free2.7023453
X-RAY DIFFRACTIONr_sphericity_bonded2.28232147
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 195 -
Rwork0.222 4413 -
obs--99.98 %

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