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- PDB-4z2v: Crystal structure of short hoefavidin-hoef-peptide complex -

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Basic information

Entry
Database: PDB / ID: 4z2v
TitleCrystal structure of short hoefavidin-hoef-peptide complex
Components
  • Avidin family
  • Hoef-peptide
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: 1.39 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 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jan 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 1.4Nov 20, 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
P: Hoef-peptide
B: Avidin family
C: Hoef-peptide


Theoretical massNumber of molelcules
Total (without water)31,1544
Polymers31,1544
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-31 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.740, 60.740, 166.800
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: Protein/peptide Hoef-peptide


Mass: 1235.339 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hoeflea phototrophica DFL-43 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A9D857*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M Bis-Tris pH 6.2-7.0 and 1.1-1.5 M ammonium sulfate
PH range: 6.2-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.39→57.07 Å / Num. obs: 61114 / % possible obs: 95 % / Redundancy: 5.2 % / Rsym value: 0.032 / Net I/σ(I): 19.4
Reflection shellResolution: 1.39→1.43 Å

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Processing

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

4z27


Resolution: 1.39→57.07 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.008 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18659 3089 5.1 %RANDOM
Rwork0.16024 ---
obs0.16161 57864 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.808 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0 Å2
2--0.27 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.39→57.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 128 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022118
X-RAY DIFFRACTIONr_bond_other_d0.0010.021829
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9132896
X-RAY DIFFRACTIONr_angle_other_deg0.83234218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39626.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02515289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02517
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_it3.8382.0291094
X-RAY DIFFRACTIONr_mcbond_other3.8392.0271093
X-RAY DIFFRACTIONr_mcangle_it4.5723.0421361
X-RAY DIFFRACTIONr_mcangle_other4.5713.0431362
X-RAY DIFFRACTIONr_scbond_it4.22.2031024
X-RAY DIFFRACTIONr_scbond_other4.1642.1961022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0013.2091534
X-RAY DIFFRACTIONr_long_range_B_refined5.31116.9032380
X-RAY DIFFRACTIONr_long_range_B_other5.30216.7152336
X-RAY DIFFRACTIONr_rigid_bond_restr6.39433947
X-RAY DIFFRACTIONr_sphericity_free23.994539
X-RAY DIFFRACTIONr_sphericity_bonded11.80953979
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 160 -
Rwork0.253 3080 -
obs--70.21 %

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