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- PDB-3ew2: Crystal structure of rhizavidin-biotin complex -

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Basic information

Entry
Database: PDB / ID: 3ew2
TitleCrystal structure of rhizavidin-biotin complex
Componentsrhizavidin
KeywordsUNKNOWN FUNCTION / high affinity / rhizavidin / biotin / avidin / streptavidin
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Hypothetical conserved protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLivnah, O. / Meir, A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of rhizavidin: insights into the enigmatic high-affinity interaction of an innate biotin-binding protein dimer.
Authors: Meir, A. / Helppolainen, S.H. / Podoly, E. / Nordlund, H.R. / Hytonen, V.P. / Maatta, J.A. / Wilchek, M. / Bayer, E.A. / Kulomaa, M.S. / Livnah, O.
History
DepositionOct 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rhizavidin
B: rhizavidin
C: rhizavidin
D: rhizavidin
E: rhizavidin
F: rhizavidin
G: rhizavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,87014
Polymers101,1607
Non-polymers1,7107
Water2,198122
1
A: rhizavidin
B: rhizavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3914
Polymers28,9032
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-17 kcal/mol
Surface area11870 Å2
MethodPISA
2
C: rhizavidin
D: rhizavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3914
Polymers28,9032
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-11 kcal/mol
Surface area10190 Å2
MethodPISA
3
E: rhizavidin
hetero molecules

E: rhizavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3914
Polymers28,9032
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2690 Å2
ΔGint-17 kcal/mol
Surface area11330 Å2
MethodPISA
4
F: rhizavidin
G: rhizavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3914
Polymers28,9032
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-11 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.654, 130.035, 237.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
rhizavidin


Mass: 14451.398 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / Gene: RHE_PD00032 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8KKW2
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 6000, 0.1M bis-tris, 0.15M NaCl, 10mM sodium phsophate, 3mM DTT., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2007
RadiationMonochromator: synchrotron optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 31739 / Num. obs: 31739 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 92.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.885 / SU B: 9.47 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.552 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30432 1608 5.1 %RANDOM
Rwork0.21319 ---
all0.2177 31739 --
obs0.2177 30099 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.002 Å2
Baniso -1Baniso -2Baniso -3
1-4.83 Å20 Å20 Å2
2---2.08 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6002 0 112 122 6236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9068555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7155791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60326.109311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5815824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8891514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024983
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.22853
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24195
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3490.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.991.54005
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70426273
X-RAY DIFFRACTIONr_scbond_it1.97632678
X-RAY DIFFRACTIONr_scangle_it2.9544.52282
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 135 -
Rwork0.246 1997 -
obs--92.41 %

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