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- PDB-1y52: structure of insect cell (Baculovirus) expressed AVR4 (C122S)-bio... -

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Basic information

Entry
Database: PDB / ID: 1y52
Titlestructure of insect cell (Baculovirus) expressed AVR4 (C122S)-biotin complex
ComponentsAvidin-related protein 4/5
KeywordsSUGAR BINDING PROTEIN / avidin / avr4 / streptavidin / high-affinity / hyper thermostability
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
BIOTIN / Avidin-related protein 4/5
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEisenberg-Domovich, Y. / Hytonen, V.P. / Wilchek, M. / Bayer, E.A. / Kulomaa, M.S. / Livnah, O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability.
Authors: Eisenberg-Domovich, Y. / Hytonen, V.P. / Wilchek, M. / Bayer, E.A. / Kulomaa, M.S. / Livnah, O.
History
DepositionDec 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Jan 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Avidin-related protein 4/5
Y: Avidin-related protein 4/5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6918
Polymers28,3182
Non-polymers1,3736
Water2,180121
1
X: Avidin-related protein 4/5
Y: Avidin-related protein 4/5
hetero molecules

X: Avidin-related protein 4/5
Y: Avidin-related protein 4/5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,38316
Polymers56,6364
Non-polymers2,74712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area14150 Å2
ΔGint-24 kcal/mol
Surface area20060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.963, 80.963, 140.698
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 -Y+1,-X+1,-Z+1

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Components

#1: Protein Avidin-related protein 4/5


Mass: 14158.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVR4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P56734
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0M ammonium sulfate,0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 51814 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Rsym value: 0.046
Reflection shellResolution: 1.7→1.73 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.537 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.076 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20038 2645 5.1 %RANDOM
Rwork0.19293 ---
all0.209 ---
obs0.19332 49130 99.52 %-
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: 29.533 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 88 121 2103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212036
X-RAY DIFFRACTIONr_bond_other_d0.0020.021784
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9642768
X-RAY DIFFRACTIONr_angle_other_deg0.9234125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3055239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3980.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022184
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02430
X-RAY DIFFRACTIONr_nbd_refined0.190.2305
X-RAY DIFFRACTIONr_nbd_other0.2550.22046
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0860.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0651.51186
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99921920
X-RAY DIFFRACTIONr_scbond_it2.6013850
X-RAY DIFFRACTIONr_scangle_it4.2884.5847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 203
Rwork0.258 3556

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