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- PDB-4i60: Crystal structure of avidin - biotinylruthenocene complex -

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Basic information

Entry
Database: PDB / ID: 4i60
TitleCrystal structure of avidin - biotinylruthenocene complex
ComponentsAvidin
KeywordsBiotin-binding protein / Beta barrel / Biotinylruthenocene / Glycoprotein / Hen egg white
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: 2.5 Å
AuthorsStrzelczyk, P. / Bujacz, A. / Bujacz, G.
CitationJournal: Chem.Biol.Interact / Year: 2013
Title: Structural investigation of the interactions of biotinylruthenocene with avidin.
Authors: Strzelczyk, P. / Bujacz, A. / Plazuk, D. / Zakrzewski, J. / Bujacz, G.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1953
Polymers14,3211
Non-polymers8742
Water1,15364
1
A: Avidin
hetero molecules

A: Avidin
hetero molecules

A: Avidin
hetero molecules

A: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,78012
Polymers57,2844
Non-polymers3,4968
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area11980 Å2
ΔGint-23 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.220, 60.220, 62.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

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Components

#1: Protein Avidin


Mass: 14321.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P02701
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-B1R / [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}cyclopentadienyl]ruthenium / biotinylruthenocene


Mass: 449.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16N2O2RuS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXPERIMENTAL INFO OF UNIPROT (P02701, AVID_CHICK) SHOWS R-> K AT POSITION 50, I -> T AT POSITION 58.

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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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% pentaerythritol propoxylate, 0.05M HEPES, 0.2M KCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 2.5→43.36 Å / Num. all: 4308 / Num. obs: 4301 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.07 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 19.49
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 8.59 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 4.75 / Num. unique all: 458 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYO

1vyo


Resolution: 2.5→43.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.912 / SU B: 16.712 / SU ML: 0.197 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21103 216 5 %RANDOM
Rwork0.16469 ---
all0.16711 4308 --
obs0.16711 4085 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 54 64 1124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021101
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.8311543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8685129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37223.91346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.80815183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.83157
X-RAY DIFFRACTIONr_chiral_restr0.1220.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0390.02802
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 13 -
Rwork0.28 245 -
obs--99.23 %
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)
13.03761.35911.10895.2333-1.5914.9097-0.0288-0.13560.13640.4126-0.0419-0.2336-0.24770.19660.07070.0703-0.0317-0.04790.1291-0.0310.06745.055539.546311.4245
25.9642-1.9918-1.71284.89241.3975.50410.0899-0.11720.3991-0.0563-0.02760.0981-0.3619-0.137-0.06230.0821-0.034-0.04450.04090.02460.080237.778742.13698.6394
32.5651-0.3921-0.47242.68521.49131.96040.106-0.1308-0.16310.251-0.0912-0.1520.2222-0.0927-0.01480.041-0.0244-0.02570.02170.02820.054640.789231.34045.1788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 46
2X-RAY DIFFRACTION2A47 - 95
3X-RAY DIFFRACTION3A96 - 128

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