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- PDB-1y53: Crystal structure of bacterial expressed avidin related protein 4... -

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Basic information

Entry
Database: PDB / ID: 1y53
TitleCrystal structure of bacterial expressed avidin related protein 4 (AVR4) C122S
ComponentsAvidin-related protein 4/5
KeywordsSUGAR BINDING PROTEIN / avidin / streptavidin / avidin related protein / high affinity / thermal stability
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
FORMIC ACID / Avidin-related protein 4/5
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 1.3Nov 10, 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

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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)28,5948
Polymers28,3182
Non-polymers2766
Water3,081171
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)57,18816
Polymers56,6364
Non-polymers55212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area12090 Å2
ΔGint-77 kcal/mol
Surface area19500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.040, 78.040, 110.979
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+1/2

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Components

#1: Protein Avidin-related protein 4/5


Mass: 14158.945 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 58.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2M sodium formate, 0.1M sodium acetate, pH 4.2, 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: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.2→40 Å / Num. obs: 107239 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rsym value: 0.065
Reflection shellResolution: 1.2→1.22 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→39.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.391 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18506 5341 5 %RANDOM
Rwork0.17686 ---
all0.178 ---
obs0.17728 101696 99.85 %-
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: 13.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.2→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 18 171 2085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211956
X-RAY DIFFRACTIONr_bond_other_d0.0020.021721
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9162647
X-RAY DIFFRACTIONr_angle_other_deg0.82833989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935239
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_restr0.4410.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022152
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02430
X-RAY DIFFRACTIONr_nbd_refined0.2170.2314
X-RAY DIFFRACTIONr_nbd_other0.2610.22049
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9591.51198
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60621922
X-RAY DIFFRACTIONr_scbond_it1.8993758
X-RAY DIFFRACTIONr_scangle_it2.7914.5724
X-RAY DIFFRACTIONr_rigid_bond_restr1.09821956
X-RAY DIFFRACTIONr_sphericity_free2.9122171
X-RAY DIFFRACTIONr_sphericity_bonded2.1121915
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.202 397
Rwork0.194 7374

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