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- PDB-4z27: Crystal structure of apo short hoefavidin -

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Basic information

Entry
Database: PDB / ID: 4z27
TitleCrystal structure of apo short hoefavidin
ComponentsAvidin family
KeywordsBiotin-binding protein / high affinity system / bacterial avidins
Function / homology
Function and homology information


biotin binding / protein homodimerization activity / 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
Biological speciesHoeflea phototrophica DFL-43 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsLivnah, O. / Avraham, O.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail.
Authors: Avraham, O. / Meir, A. / Fish, A. / Bayer, E.A. / Livnah, O.
History
DepositionMar 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avidin family
B: Avidin family


Theoretical massNumber of molelcules
Total (without water)28,6832
Polymers28,6832
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-18 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.170, 61.170, 166.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Avidin family


Mass: 14341.508 Da / Num. of mol.: 2 / Fragment: UNP residues 21-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hoeflea phototrophica DFL-43 (bacteria)
Gene: HPDFL43_17171 / Production host: Escherichia coli (E. coli) / References: UniProt: A9D857
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Streak seeding was applied with source crystals. Crystals appeared within 24 hours and grew to their maximal size within 2 weeks

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.34→57.4 Å / Num. obs: 72099 / % possible obs: 95.6 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.1
Reflection shellResolution: 1.34→1.39 Å / Rmerge(I) obs: 0.564

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOSFLMdata reduction
MOLREPphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z6J

4z6j


Resolution: 1.34→57.42 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.793 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18904 3408 5 %RANDOM
Rwork0.1652 ---
obs0.16634 65432 95.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å2-0 Å2
2--0.42 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.34→57.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 0 115 2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021955
X-RAY DIFFRACTIONr_bond_other_d0.0010.021672
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9052673
X-RAY DIFFRACTIONr_angle_other_deg0.94733852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6332690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48415263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02495
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4282.1051004
X-RAY DIFFRACTIONr_mcbond_other3.4192.1021003
X-RAY DIFFRACTIONr_mcangle_it4.3113.181252
X-RAY DIFFRACTIONr_mcangle_other4.313.1811253
X-RAY DIFFRACTIONr_scbond_it3.3962.25951
X-RAY DIFFRACTIONr_scbond_other3.3952.25952
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9473.2691421
X-RAY DIFFRACTIONr_long_range_B_refined4.6717.3762161
X-RAY DIFFRACTIONr_long_range_B_other4.6517.2212130
X-RAY DIFFRACTIONr_rigid_bond_restr4.07233627
X-RAY DIFFRACTIONr_sphericity_free23.745548
X-RAY DIFFRACTIONr_sphericity_bonded12.35153636
LS refinement shellResolution: 1.34→1.375 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 252 -
Rwork0.281 4626 -
obs--93.32 %

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