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- PDB-2y3e: Traptavidin, apo-form -

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Basic information

Entry
Database: PDB / ID: 2y3e
TitleTraptavidin, apo-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
Biological speciesSTREPTOMYCES AVIDINII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 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. THE SHEETS PRESENTED AS "BA" 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
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6155
Polymers28,3392
Non-polymers2763
Water5,729318
1
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,23010
Polymers56,6774
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area11060 Å2
ΔGint-65.3 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.594, 57.594, 183.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.00019, 1, -0.00055), (1, 0.00019, -0.00194), (-0.00194, -0.00055, -1)
Vector: -0.00391, -0.05743, -23.49617)

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Components

#1: Protein STREPTAVIDIN / TRAPTAVIDIN


Mass: 14169.281 Da / Num. of mol.: 2 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 318 / 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 ...ENGINEERED RESIDUE IN CHAIN A, SER 76 TO GLY ENGINEERED RESIDUE IN CHAIN A, ARG 77 TO ASP ENGINEERED RESIDUE IN CHAIN B, SER 76 TO GLY ENGINEERED RESIDUE IN CHAIN B, 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: 2.88 Å3/Da / Density % sol: 57.3 % / Description: NONE
Crystal growpH: 7.5
Details: 12% PEG 8000, 9% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.5

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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
Reflection twinOperator: -H,K,-L / Fraction: 0.497
ReflectionResolution: 1.45→27.47 Å / Num. obs: 51553 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 16.65 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 87.1

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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 1SWB

1swb


Resolution: 1.449→27.474 Å / σ(F): 0.02 / Phase error: 21.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1782 2616 5.3 %
Rwork0.1342 --
obs0.1353 48884 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.048 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 33.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.77 Å20 Å20 Å2
2---2.77 Å20 Å2
3----11.8633 Å2
Refinement stepCycle: LAST / Resolution: 1.449→27.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 18 318 2122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051925
X-RAY DIFFRACTIONf_angle_d0.9342643
X-RAY DIFFRACTIONf_dihedral_angle_d14.479610
X-RAY DIFFRACTIONf_chiral_restr0.062289
X-RAY DIFFRACTIONf_plane_restr0.003337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4511-1.4790.32191030.26961763X-RAY DIFFRACTION60
1.479-1.50920.33081340.25352087X-RAY DIFFRACTION73
1.5092-1.5420.2651300.22472425X-RAY DIFFRACTION83
1.542-1.57780.27051330.22412452X-RAY DIFFRACTION85
1.5778-1.61730.2621440.21582528X-RAY DIFFRACTION86
1.6173-1.6610.26481290.212549X-RAY DIFFRACTION88
1.661-1.70990.27451210.20052581X-RAY DIFFRACTION90
1.7099-1.76510.21541410.19152668X-RAY DIFFRACTION90
1.7651-1.82810.22111350.18272650X-RAY DIFFRACTION92
1.8281-1.90130.20741540.17142716X-RAY DIFFRACTION93
1.9013-1.98780.18531430.15762721X-RAY DIFFRACTION93
1.9878-2.09250.18721630.14472700X-RAY DIFFRACTION93
2.0925-2.22350.17791350.13992764X-RAY DIFFRACTION94
2.2235-2.39510.16831100.13532787X-RAY DIFFRACTION95
2.3951-2.63580.18821510.11992743X-RAY DIFFRACTION94
2.6358-3.01650.15311450.10512746X-RAY DIFFRACTION94
3.0165-3.7980.14251460.08052754X-RAY DIFFRACTION94
3.798-23.73840.12911720.0882733X-RAY DIFFRACTION93

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