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- PDB-2y3f: Traptavidin, biotin bound form -

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Basic information

Entry
Database: PDB / ID: 2y3f
TitleTraptavidin, biotin bound form
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN / PROTEIN ENGINEERING
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesSTREPTOMYCES AVIDINII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.493 Å
AuthorsChivers, C.E. / Koner, A.L. / Lowe, E.D. / Howarth, M.
CitationJournal: Biochem.J. / Year: 2011
Title: How the Biotin-Streptavidin Interaction Was Made Even Stronger: Investigation Via Crystallography and a Chimeric Tetramer.
Authors: Chivers, C.E. / Koner, A.L. / Lowe, E.D. / Howarth, M.
History
DepositionDec 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6905
Polymers14,1691
Non-polymers5214
Water2,162120
1
A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,75920
Polymers56,6774
Non-polymers2,08216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area14860 Å2
ΔGint-50.6 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.340, 57.340, 77.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

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Components

#1: Protein STREPTAVIDIN / TRAPTAVIDIN


Mass: 14169.281 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-163 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: STREPTAVIDIN MUTATED TO INCREASE BIOTIN BINDING AFFINITY
Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RIPL / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 76 TO GLY ENGINEERED RESIDUE IN CHAIN A, ARG 77 TO ASP

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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: 2.41 Å3/Da / Density % sol: 49.09 % / Description: NONE
Crystal growpH: 8.5 / Details: 27% PEG 4000, 0.25M MGCL2, 0.1M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 6, 2009
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→38.78 Å / Num. obs: 21720 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 7.45 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 19.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3E

2y3e


Resolution: 1.493→32.12 Å / SU ML: 0.16 / σ(F): 0.09 / Phase error: 10.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1515 1107 5.1 %
Rwork0.1349 --
obs0.1358 21581 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.003 Å2 / ksol: 0.454 e/Å3
Displacement parametersBiso mean: 12.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.8611 Å20 Å2-0 Å2
2--0.8611 Å20 Å2
3----8.1285 Å2
Refinement stepCycle: LAST / Resolution: 1.493→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 34 120 1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091016
X-RAY DIFFRACTIONf_angle_d1.4821396
X-RAY DIFFRACTIONf_dihedral_angle_d12.852331
X-RAY DIFFRACTIONf_chiral_restr0.094155
X-RAY DIFFRACTIONf_plane_restr0.005176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.493-1.56090.12511470.08042496X-RAY DIFFRACTION99
1.5609-1.64320.14441280.08462490X-RAY DIFFRACTION99
1.6432-1.74620.14181630.09142485X-RAY DIFFRACTION99
1.7462-1.8810.14191330.09672517X-RAY DIFFRACTION100
1.881-2.07030.10991270.10382555X-RAY DIFFRACTION100
2.0703-2.36980.11951540.11892549X-RAY DIFFRACTION100
2.3698-2.98530.15981210.14342623X-RAY DIFFRACTION100
2.9853-32.12770.18221340.17242759X-RAY DIFFRACTION100

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