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- PDB-4z28: Crystal structure of short hoefavidin biotin complex -

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Basic information

Entry
Database: PDB / ID: 4z28
TitleCrystal structure of short hoefavidin biotin complex
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: 1.66 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 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Jan 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 1.3Nov 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5906
Polymers28,6832
Non-polymers9074
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-3 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.180, 61.180, 166.860
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 / short-hoefavidin


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: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 54.81 %
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: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 38372 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.9
Reflection shellResolution: 1.66→1.72 Å / Rmerge(I) obs: 0.798

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOSFLMdata reduction
MOLREPphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z27

4z27


Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.661 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23017 1924 5 %RANDOM
Rwork0.17955 ---
obs0.18194 36448 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.531 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å20 Å2
2---2.02 Å2-0 Å2
3---4.05 Å2
Refinement stepCycle: 1 / Resolution: 1.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 60 78 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022032
X-RAY DIFFRACTIONr_bond_other_d0.0020.021747
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9352774
X-RAY DIFFRACTIONr_angle_other_deg1.48634035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76126.04491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64315265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212401
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02507
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_it5.3373.1611012
X-RAY DIFFRACTIONr_mcbond_other5.3313.1581011
X-RAY DIFFRACTIONr_mcangle_it6.4484.7691262
X-RAY DIFFRACTIONr_mcangle_other6.4514.7711263
X-RAY DIFFRACTIONr_scbond_it7.6193.4021020
X-RAY DIFFRACTIONr_scbond_other7.6193.4021020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9314.9911512
X-RAY DIFFRACTIONr_long_range_B_refined7.10526.3552166
X-RAY DIFFRACTIONr_long_range_B_other7.1126.2392146
X-RAY DIFFRACTIONr_rigid_bond_restr4.34433779
X-RAY DIFFRACTIONr_sphericity_free42.702522
X-RAY DIFFRACTIONr_sphericity_bonded26.69353776
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 140 -
Rwork0.276 2620 -
obs--99.5 %

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