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Basic information

Entry
Database: PDB / ID: 1wbi
TitleAVR2
ComponentsAVIDIN-RELATED PROTEIN 2
KeywordsAVIDIN-RELATED PROTEIN / AVIDIN RELATED PROTEIN / BIOTIN
Function / homology
Function and homology information


biotin transport / 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 ...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 2
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAirenne, T.T. / Hytonen, V.P. / Maatta, J.H. / Kidron, H. / Halling, K.K. / Horha, J. / Kulomaa, T. / Nyholm, T.K.M. / Johnson, M.S. / Salminen, T.A. / Kulomaa, M.S.
CitationJournal: Bmc Biotechnol. / Year: 2005
Title: Avidin Related Protein 2 Shows Unique Structural and Functional Features Among the Avidin Protein Family.
Authors: Hytonen, V.P. / Maatta, J.A. / Kidron, H. / Halling, K.K. / Horha, J. / Kulomaa, T. / Nyholm, T.K.M. / Johnson, M.S. / Salminen, T.A. / Kulomaa, M.S. / Airenne, T.T.
History
DepositionNov 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA EA FA GA HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BYA 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AVIDIN-RELATED PROTEIN 2
B: AVIDIN-RELATED PROTEIN 2
C: AVIDIN-RELATED PROTEIN 2
D: AVIDIN-RELATED PROTEIN 2
E: AVIDIN-RELATED PROTEIN 2
F: AVIDIN-RELATED PROTEIN 2
G: AVIDIN-RELATED PROTEIN 2
H: AVIDIN-RELATED PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,42636
Polymers114,5748
Non-polymers3,85228
Water21,0421168
1
A: AVIDIN-RELATED PROTEIN 2
B: AVIDIN-RELATED PROTEIN 2
C: AVIDIN-RELATED PROTEIN 2
D: AVIDIN-RELATED PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,20918
Polymers57,2874
Non-polymers1,92214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: AVIDIN-RELATED PROTEIN 2
F: AVIDIN-RELATED PROTEIN 2
G: AVIDIN-RELATED PROTEIN 2
H: AVIDIN-RELATED PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,21718
Polymers57,2874
Non-polymers1,93014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.669, 99.936, 135.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96029, -0.06927, -0.27026), (-0.06995, -0.87797, 0.47358), (-0.27008, 0.47368, 0.83826)126.92196, 45.78107, 6.748
2given(-0.78516, 0.60704, -0.12261), (0.60604, 0.7124, -0.35383), (-0.12744, -0.35212, -0.92724)98.64066, -28.70881, 30.16248
3given(0.75067, -0.52917, 0.39557), (-0.53114, -0.83944, -0.115), (0.39291, -0.12377, -0.91121)25.51218, 78.13982, -8.14122
4given(-0.59988, -0.79103, -0.12008), (-0.70637, 0.59409, -0.38484), (0.37575, -0.14604, -0.91514)104.57023, 93.51885, -40.66335
5given(-0.05586, 0.99801, -0.0293), (-0.99834, -0.05541, 0.01573), (0.01408, 0.03013, 0.99945)27.10779, 124.5086, -35.80017
6given(0.65267, 0.68613, -0.3213), (0.74914, -0.64779, 0.13841), (-0.11317, -0.33104, -0.93681)-7.98308, 27.92414, -5.27176
7given(0.00705, -0.88393, 0.46757), (0.9625, 0.1328, 0.23655), (-0.27119, 0.44837, 0.85172)64.44987, -4.89625, -26.79245

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Components

#1: Protein
AVIDIN-RELATED PROTEIN 2 / AVR2


Mass: 14321.787 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P56732
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1168 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.28 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. obs: 257876 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYO

1vyo


Resolution: 1.4→81.65 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.055 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 12894 5 %RANDOM
Rwork0.174 ---
obs0.175 244972 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.4→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7573 0 234 1168 8975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0218113
X-RAY DIFFRACTIONr_bond_other_d0.0020.027071
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.94411037
X-RAY DIFFRACTIONr_angle_other_deg0.869316500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79324.621396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.874151298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0431549
X-RAY DIFFRACTIONr_chiral_restr0.1080.21247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028885
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021644
X-RAY DIFFRACTIONr_nbd_refined0.1910.21360
X-RAY DIFFRACTIONr_nbd_other0.2020.27416
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23707
X-RAY DIFFRACTIONr_nbtor_other0.0860.24757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2860
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.361.56143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63927839
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.40233874
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5084.53198
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 938
Rwork0.313 17825

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