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- PDB-2of8: Crystal structure of AVR4 (D39A/C122S)-BNA complex -

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Basic information

Entry
Database: PDB / ID: 2of8
TitleCrystal structure of AVR4 (D39A/C122S)-BNA complex
ComponentsAvidin-related protein 4/5
KeywordsLIGAND BINDING PROTEIN / avidin / streptavidin / AVR4 / high affinity / pseudo-catalysis
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 / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsLivnah, O. / Hayouka, R. / Eisenberg-Domovich, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester.
Authors: Hayouka, R. / Eisenberg-Domovich, Y. / Hytonen, V.P. / Maatta, J.A. / Nordlund, H.R. / Kulomaa, M.S. / Wilchek, M. / Bayer, E.A. / Livnah, O.
History
DepositionJan 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)29,46515
Polymers28,2302
Non-polymers1,23513
Water4,414245
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)58,93030
Polymers56,4604
Non-polymers2,47026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)78.175, 78.175, 110.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailshe second part of the biological assembly is generated by the two fold axis: Y+1, -X+1, -Z+0.5

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Components

#1: Protein Avidin-related protein 4/5


Mass: 14114.935 Da / Num. of mol.: 2 / Mutation: D39A, C122S, D239A, C322S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVR4 / Plasmid: pET101/D-TOPOR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AITM / 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


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.5-1.9M NaFormat, 0.1M Acetate, PH 4.2-4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9253
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9253 Å / Relative weight: 1
ReflectionResolution: 1.05→63.25 Å / Num. all: 150801 / Num. obs: 150801 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 47.5
Reflection shellResolution: 1.05→1.09 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.05→63.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.267 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17659 7965 5 %RANDOM
Rwork0.16343 ---
all0.165 ---
obs0.16408 150801 99.94 %-
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: 10.892 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.05→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 50 278 2274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212078
X-RAY DIFFRACTIONr_bond_other_d0.0030.021819
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9472817
X-RAY DIFFRACTIONr_angle_other_deg0.94634226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955255
X-RAY DIFFRACTIONr_chiral_restr0.4640.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022284
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02446
X-RAY DIFFRACTIONr_nbd_refined0.1960.2367
X-RAY DIFFRACTIONr_nbd_other0.2560.22266
X-RAY DIFFRACTIONr_nbtor_other0.0850.21232
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.222
X-RAY DIFFRACTIONr_mcbond_it0.881.51256
X-RAY DIFFRACTIONr_mcangle_it1.51422010
X-RAY DIFFRACTIONr_scbond_it1.753822
X-RAY DIFFRACTIONr_scangle_it2.6314.5806
X-RAY DIFFRACTIONr_rigid_bond_restr0.92722078
X-RAY DIFFRACTIONr_sphericity_free2.2852245
X-RAY DIFFRACTIONr_sphericity_bonded2.09122030
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 557
Rwork0.252 11002

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