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- PDB-3fdc: Crystal Structure of Avidin -

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Basic information

Entry
Database: PDB / ID: 3fdc
TitleCrystal Structure of Avidin
ComponentsAvidin
KeywordsPROTEIN BINDING / beta barrel / Biotin / Glycoprotein / Polymorphism / Secreted
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsBarker, K.D. / Sazinsky, M.H. / Eckermann, A.L. / Abajian, C. / Hartings, M.R. / Rosenzweig, A.C. / Meade, T.J.
CitationJournal: Bioconjug.Chem. / Year: 2009
Title: Protein Binding and the Electronic Properties of Iron(II) Complexes: An Electrochemical and Optical Investigation of Outer Sphere Effects.
Authors: Barker, K.D. / Eckermann, A.L. / Sazinsky, M.H. / Hartings, M.R. / Abajian, C. / Georganopoulou, D. / Ratner, M.A. / Rosenzweig, A.C. / Meade, T.J.
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Avidin
B: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8714
Polymers28,7002
Non-polymers1,1712
Water25214
1
A: Avidin
B: Avidin
hetero molecules

A: Avidin
B: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7428
Polymers57,4004
Non-polymers2,3424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area9940 Å2
ΔGint-41 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.200, 74.200, 85.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Avidin


Mass: 14350.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02701
#2: Chemical ChemComp-BTF / iron(II) tetracyano-5-(2-Oxo-hexahydro-thieno[3,4-d]imidazol-6-yl)-pentanoic acid (4'-methyl-[2,2']bipyridinyl-4-ylmethyl)-amide


Mass: 585.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27FeN9O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDISTANCE BETWEEN C16 AND C19 ATOMS OF BTF129 IS 1.85A FOR CHAIN B AND 1.81A FOR CHAIN A.
Sequence detailsRESIDUE A ILE 56 AND RESIDUE A ASN 57 ARE NOT LINKED PROPERLY. DISTANCE OF C-N BOND IS 1.72A.

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% PEG 3000, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 296.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.279 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.279 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 5233 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.099 / Rsym value: 0.095 / Net I/σ(I): 28

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
PHASERphasing
RefinementStarting model: PDB ENTRY 1LDO

1ldo


Resolution: 3.1→30 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflectionSelection details
Rfree0.33 --RANDOM
Rwork0.255 ---
obs-5233 99.9 %-
Displacement parametersBiso max: 118.17 Å2 / Biso mean: 64.302 Å2 / Biso min: 10.6 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 61 14 1923
LS refinement shellResolution: 3.1→3.27 Å
RfactorNum. reflection% reflection
Rfree0.424 92 -
Rwork0.424 --
obs-742 99.9 %

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