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- PDB-3ew1: Crystal structure of rhizavidin -

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Basic information

Entry
Database: PDB / ID: 3ew1
TitleCrystal structure of rhizavidin
Componentsrhizavidin
KeywordsUNKNOWN FUNCTION / high affinity / rhizavidin / biotin / avidin
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
Hypothetical conserved protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Derived calculations / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)86,7086
Polymers86,7086
Non-polymers00
Water12,863714
1
A: rhizavidin
B: rhizavidin


Theoretical massNumber of molelcules
Total (without water)28,9032
Polymers28,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-16 kcal/mol
Surface area12950 Å2
2
C: rhizavidin
D: rhizavidin


Theoretical massNumber of molelcules
Total (without water)28,9032
Polymers28,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-16 kcal/mol
Surface area13820 Å2
3
E: rhizavidin
F: rhizavidin


Theoretical massNumber of molelcules
Total (without water)28,9032
Polymers28,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-16 kcal/mol
Surface area14110 Å2
4
B: rhizavidin
E: rhizavidin

D: rhizavidin
F: rhizavidin


Theoretical massNumber of molelcules
Total (without water)57,8064
Polymers57,8064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area8740 Å2
ΔGint-51 kcal/mol
Surface area25240 Å2
MethodPISA
5
A: rhizavidin


Theoretical massNumber of molelcules
Total (without water)14,4511
Polymers14,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
B: rhizavidin


Theoretical massNumber of molelcules
Total (without water)14,4511
Polymers14,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
C: rhizavidin


Theoretical massNumber of molelcules
Total (without water)14,4511
Polymers14,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
D: rhizavidin


Theoretical massNumber of molelcules
Total (without water)14,4511
Polymers14,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
E: rhizavidin


Theoretical massNumber of molelcules
Total (without water)14,4511
Polymers14,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
10
F: rhizavidin


Theoretical massNumber of molelcules
Total (without water)14,4511
Polymers14,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.834, 116.851, 48.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-874-

HOH

21F-785-

HOH

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Components

#1: Protein
rhizavidin


Mass: 14451.398 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 1.91 Å3/Da / Density % sol: 35.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 4000, 0.1M Tris-HCl. 0.2M MgCl2, 5mM DTT, pH 8.0, 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: 1.5→45.08 Å / Num. all: 104982 / Num. obs: 99649 / % possible obs: 98.1 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 90.6

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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: 1.5→45.08 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.779 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 5320 5.1 %RANDOM
Rwork0.16834 ---
obs0.17112 99649 98.16 %-
all-104982 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 0 714 6756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.621.8918930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40726.35326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78815917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6961512
X-RAY DIFFRACTIONr_chiral_restr0.1310.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025303
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22918
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24578
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2601
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.2126
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5771.54274
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27826755
X-RAY DIFFRACTIONr_scbond_it3.24132638
X-RAY DIFFRACTIONr_scangle_it4.3494.52175
X-RAY DIFFRACTIONr_rigid_bond_restr1.75536912
X-RAY DIFFRACTIONr_sphericity_free7.5373714
X-RAY DIFFRACTIONr_sphericity_bonded6.94536332
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 343 -
Rwork0.256 6598 -
obs--88.77 %

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