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- PDB-1vyo: Crystal structure of avidin -

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Basic information

Entry
Database: PDB / ID: 1vyo
TitleCrystal structure of avidin
ComponentsAVIDIN
KeywordsGLYCOPROTEIN / BIOTIN
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / 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
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsAirenne, T.T. / Johnson, M.S. / Salminen, T.A.
CitationJournal: Chem.Biol. / Year: 2006
Title: Binding Properties of Haba-Type Azo Derivatives to Avidin and Avidin-Related Protein 4.
Authors: Repo, S. / Paldanius, T.A. / Hytonen, V.P. / Nyholm, T.K. / Halling, K.K. / Huuskonen, J. / Pentikainen, O.T. / Rissanen, K. / Slotte, J.P. / Airenne, T.T. / Salminen, T.A. / Kulomaa, M.S. / Johnson, M.S.
History
DepositionMay 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details ..._exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _reflns_shell.Rmerge_I_obs
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2758
Polymers28,7222
Non-polymers5536
Water2,684149
1
A: AVIDIN
B: AVIDIN
hetero molecules

A: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,55016
Polymers57,4454
Non-polymers1,10512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12110 Å2
ΔGint-58.1 kcal/mol
Surface area23550 Å2
MethodPQS
Unit cell
Length a, b, c (Å)72.949, 78.772, 43.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.2391, 0.971, 0.0016), (0.971, 0.2391, -0.0037), (-0.004, 0.0007, -1)
Vector: 0.0169, 0.0719, 14.8821)

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Components

#1: Protein AVIDIN


Mass: 14361.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02701
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: THE BIOLOGICAL FUNCTION OF AVIDIN IS NOT KNOWN. FORMS A STRONG NON-COVALENT SPECIFIC ...FUNCTION: THE BIOLOGICAL FUNCTION OF AVIDIN IS NOT KNOWN. FORMS A STRONG NON-COVALENT SPECIFIC COMPLEX WITH BIOTIN (ONE MOLECULE OF BIOTIN PER SUBUNIT OF AVIDIN).

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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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Equal volumes (1 ul) of protein (0.5 mg/ml) in 50 mM Na acetate (pH 4) + 20 mM NaCl and well solution of 0.1 M MES (pH 6.6) + 24% PEG 8000 + 0.2 M Mg acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.804
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.804 Å / Relative weight: 1
ReflectionResolution: 1.48→20 Å / Num. obs: 41811 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10
Reflection shellResolution: 1.48→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AVD

1avd


Resolution: 1.48→19.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.213 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PEPTIDE BONDS BETWEEN RESIDUES A41 AND A42 AND BETWEEN B41 AND B42 HAVE BEEN DETERMINED TO BE CIS- BONDS. THESE RESIDUES ARE NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PEPTIDE BONDS BETWEEN RESIDUES A41 AND A42 AND BETWEEN B41 AND B42 HAVE BEEN DETERMINED TO BE CIS- BONDS. THESE RESIDUES ARE NOT EXPECTED TO ADOPT THE CIS- CONFORMATION. THIS IS DUE TO THE POOR ELECTRON DENSITY IN THESE REGIONS OF THE ELECTRON DENSITY MAP. RESIDUES 34-46 OF BOTH CHAINS FORM LOOPS WITH TWO ALTERNATE CONFORMATIONS. BOTH ALTERNATE CONFORMATIONS CAN BE DETERMINED FOR RESIDUES 34-36 AND 42-46, BUT DUE TO POOR ELECTRON DENSITY RESIDUES 37-41 CAN BE ASSIGNED ONLY A SINGLE CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2091 5 %RANDOM
Rwork0.165 ---
obs0.167 39720 100 %-
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: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---0.35 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.48→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 36 149 2090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212134
X-RAY DIFFRACTIONr_bond_other_d0.0030.021914
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9242887
X-RAY DIFFRACTIONr_angle_other_deg0.84934477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9725257
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_restr0.0970.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022290
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02427
X-RAY DIFFRACTIONr_nbd_refined0.1920.2373
X-RAY DIFFRACTIONr_nbd_other0.2570.22260
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.21330
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.249
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.2197
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.71.51285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22622114
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0133849
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2464.5773
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: 1.48→1.52 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 152
Rwork0.254 2878
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)
12.7193-1.07471.85857.32884.24087.92310.12450.2604-0.158-0.6367-0.06830.0551-0.0939-0.1316-0.05620.1457-0.0046-0.00040.18110.04020.1539-3.45416.029-8.855
22.7157-0.6074-2.0201-2.3362-0.82519.12220.0724-0.2556-0.1887-0.04430.08220.3024-0.0972-0.2961-0.15460.314-0.049-0.01160.27340.01370.282516.6310.30823.692
32.824-0.7272-0.65852.4720.16042.3247-0.0537-0.13290.17320.24740.0376-0.085-0.16890.04350.01610.1190.0169-0.0170.0919-0.00070.1117-7.89921.0988.321
42.41310.02820.29733.2377-0.78741.902-0.01310.11850.0345-0.0093-0.0988-0.269-0.08770.26240.11190.0323-0.0155-0.02180.17820.02590.146522.608-2.1565.725
51.1466-0.11270.30491.2939-0.04953.283-0.0388-0.02260.10760.1080.0334-0.0002-0.3145-0.04910.00540.03730.01770.0010.04580.00350.067-8.76513.988.801
662.416548.467.495978.852-38.012245.6776-0.1495-0.2498-1.4287-0.0179-0.3422-2.36010.64041.61840.49170.3773-0.0462-0.00020.3438-0.02240.34086.74822.81118.486
72.18870.98890.61024.30451.11121.8954-0.01520.11550.041-0.04750.0201-0.0694-0.11140.059-0.00490.00270.00930.00860.06220.01410.0351-2.8286.7082.494
81.2312-0.1023-0.33271.3649-0.32091.8257-0.0169-0.01820.06230.09940.011-0.0798-0.07260.14130.00590.0184-0.0042-0.01880.0616-0.00320.061612.239-2.0948.076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 45
2X-RAY DIFFRACTION2B34 - 45
3X-RAY DIFFRACTION3A3 - 33
4X-RAY DIFFRACTION4B2 - 33
5X-RAY DIFFRACTION5A46 - 84
6X-RAY DIFFRACTION6A85 - 90
7X-RAY DIFFRACTION7A91 - 123
8X-RAY DIFFRACTION8B46 - 123

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