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- PDB-2fhl: avidin related protein (AVR4)-BNA complex -

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Basic information

Entry
Database: PDB / ID: 2fhl
Titleavidin related protein (AVR4)-BNA complex
ComponentsAvidin-related protein 4/5
KeywordsSUGAR BINDING PROTEIN / AVIDIN / AVR4 / STREPTAVIDIN / HIGH-AFFINITY / Hydrolytic activity
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BNI / FORMIC ACID / Avidin-related protein 4/5
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsLivnah, O. / Prizant, M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Factors dictating the pseudocatalytic efficiency of avidins
Authors: Prizant, M. / Eisenberg-Domovich, Y. / Hytonen, V.P. / Kulomaa, M.S. / Wilchek, M. / Bayer, E.A. / Livnah, O.
History
DepositionDec 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avidin-related protein 4/5
B: Avidin-related protein 4/5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,59014
Polymers27,4012
Non-polymers1,18912
Water5,314295
1
A: Avidin-related protein 4/5
B: Avidin-related protein 4/5
hetero molecules

A: Avidin-related protein 4/5
B: Avidin-related protein 4/5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,18028
Polymers54,8024
Non-polymers2,37824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area16190 Å2
ΔGint-34 kcal/mol
Surface area19000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.039, 78.039, 110.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis: -Y, -X, -Z+1/2

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Components

#1: Protein Avidin-related protein 4/5


Mass: 13700.483 Da / Num. of mol.: 2 / Mutation: C122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVR4 / Production host: Escherichia coli (E. coli) / References: UniProt: P56734
#2: Chemical ChemComp-BNI / 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE / BIOTINYL P-NITROANILINE


Mass: 364.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N4O4S
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 3.0M format, 0.1 M acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.05→40 Å / Num. obs: 157254 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rsym value: 0.054 / Net I/σ(I): 34.7
Reflection shellResolution: 1.05→1.07 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1y52

1y52


Resolution: 1.05→40 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.298 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17708 7908 5 %RANDOM
Rwork0.16659 ---
all0.1675 ---
obs0.16711 149834 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.764 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 80 295 2269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212101
X-RAY DIFFRACTIONr_bond_other_d0.0030.021841
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9462846
X-RAY DIFFRACTIONr_angle_other_deg0.85334276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615255
X-RAY DIFFRACTIONr_chiral_restr0.4310.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022311
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02458
X-RAY DIFFRACTIONr_nbd_refined0.2380.2379
X-RAY DIFFRACTIONr_nbd_other0.260.22307
X-RAY DIFFRACTIONr_nbtor_other0.0840.21263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.215
X-RAY DIFFRACTIONr_mcbond_it0.8711.51256
X-RAY DIFFRACTIONr_mcangle_it1.49122015
X-RAY DIFFRACTIONr_scbond_it1.8993845
X-RAY DIFFRACTIONr_scangle_it2.9634.5830
X-RAY DIFFRACTIONr_rigid_bond_restr1.00922101
X-RAY DIFFRACTIONr_sphericity_free2.2192295
X-RAY DIFFRACTIONr_sphericity_bonded2.20722052
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 602
Rwork0.259 10911

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