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- PDB-2uz2: Crystal structure of Xenavidin -

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Basic information

Entry
Database: PDB / ID: 2uz2
TitleCrystal structure of Xenavidin
ComponentsXENAVIDIN
KeywordsGLYCOPROTEIN / BETA-BARREL / BIOTIN-BINDING PROTEIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / BIOTIN / Avd protein
Similarity search - Component
Biological speciesXENOPUS TROPICALIS (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsHelppolainen, S.H. / Maatta, J.A.E. / Airenne, T.T. / Johnson, M.S. / Kulomaa, M.S. / Nordlund, H.R.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: Structural and Functional Characteristics of Xenavidin, the First Frog Avidin from Xenopus Tropicalis.
Authors: Maatta, J.A.E. / Helppolainen, S.H. / Hytonen, V.P. / Johnson, M.S. / Kulomaa, M.S. / Airenne, T.T. / Nordlund, H.R.
History
DepositionApr 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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 "DA" 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XENAVIDIN
D: XENAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0794
Polymers29,7752
Non-polymers3032
Water3,747208
1
A: XENAVIDIN
D: XENAVIDIN
hetero molecules

A: XENAVIDIN
D: XENAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1588
Polymers59,5514
Non-polymers6074
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area11210 Å2
ΔGint-55.51 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.817, 110.817, 142.339
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99999, -0.00242, 0.00337), (-0.00342, 0.02077, -0.99978), (0.00235, -0.99978, -0.02077)
Vector: 2.21764, 78.89062, 80.49583)

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Components

#1: Protein XENAVIDIN


Mass: 14887.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS TROPICALIS (tropical clawed frog)
Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: A7YYL1*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.7 Å3/Da / Density % sol: 54.08 %
Description: ARPWARP, STARTING FROM EXISTING MODEL, WAS USED TO BUILD THE INITIAL MODEL. THE EXISTING MODEL WAS BUILT USING AN UNPUBLISHED DATA SET COLLECTED AT THE MAX-LAB BEAM LINE I911 IN JUNE ...Description: ARPWARP, STARTING FROM EXISTING MODEL, WAS USED TO BUILD THE INITIAL MODEL. THE EXISTING MODEL WAS BUILT USING AN UNPUBLISHED DATA SET COLLECTED AT THE MAX-LAB BEAM LINE I911 IN JUNE 2006 AND IS RELATED TO PDB ENTRY 2UYW.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 37060 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.491 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.42
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 8.595 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.67 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
XDSdata reduction
XSCALEdata scaling
ARP/wARPphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.523 / SU ML: 0.059 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1852 5 %RANDOM
Rwork0.181 ---
obs0.183 35206 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 20 208 2111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9262861
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17324.4998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53915366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9251511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021589
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.2933
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7441.51272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20222032
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8643947
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9154.5808
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 106
Rwork0.234 2594
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3176-0.4234-0.0232.9023-1.02462.6969-0.0696-0.08440.07220.1977-0.1266-0.52110.03310.4280.1962-0.0961-0.0001-0.0203-0.05860.048-0.16888.72524.7358.114
21.02460.553-0.01112.3732-1.04092.03780.01160.04580.0375-0.05510.05150.14050.0873-0.2396-0.0631-0.09770.00870.0051-0.11160.0192-0.2438-6.56520.90454.259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 122
2X-RAY DIFFRACTION2D5 - 123

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