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- PDB-5myq: Crystal structure of avidin in complex with ferrocene homobiotin ... -

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Basic information

Entry
Database: PDB / ID: 5myq
TitleCrystal structure of avidin in complex with ferrocene homobiotin derivative
ComponentsAvidin
KeywordsBiotin-binding protein / complex
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 ...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
ferrocene homobiotin derivative / IODIDE ION / Avidin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsStrzelczyk, P. / Bujacz, G.
CitationJournal: To Be Published
Title: Structural investigation of the interactions of ferrocene homobiotin derivative with avidin.
Authors: Strzelczyk, P. / Plazuk, D. / Bujacz, G.
History
DepositionJan 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avidin
B: Avidin
C: Avidin
D: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,55133
Polymers57,3964
Non-polymers5,15529
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-34 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.933, 82.081, 74.601
Angle α, β, γ (deg.)90.00, 106.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Avidin


Mass: 14349.097 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02701
#2: Chemical
ChemComp-HBF / ferrocene homobiotin derivative


Mass: 401.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H17FeN2OS
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium iodide, 22 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.89→71.6 Å / Num. obs: 42387 / % possible obs: 97.1 % / Redundancy: 1.92 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.36
Reflection shellRedundancy: 1.9 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.97 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYO

1vyo


Resolution: 1.89→71.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.551 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23201 1229 3.1 %RANDOM
Rwork0.18567 ---
obs0.18711 38729 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.481 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å2-0.65 Å2
2---2.08 Å2-0 Å2
3---1.04 Å2
Refinement stepCycle: 1 / Resolution: 1.89→71.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 181 337 4346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194112
X-RAY DIFFRACTIONr_bond_other_d0.0020.023808
X-RAY DIFFRACTIONr_angle_refined_deg2.1851.9395756
X-RAY DIFFRACTIONr_angle_other_deg1.11538740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4125484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50823.721172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08815676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4821528
X-RAY DIFFRACTIONr_chiral_restr0.1110.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024532
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021020
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2641.8321948
X-RAY DIFFRACTIONr_mcbond_other1.2611.831947
X-RAY DIFFRACTIONr_mcangle_it2.1332.7292428
X-RAY DIFFRACTIONr_mcangle_other2.1342.7312429
X-RAY DIFFRACTIONr_scbond_it1.5592.1612164
X-RAY DIFFRACTIONr_scbond_other1.5582.1622165
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1393.1883173
X-RAY DIFFRACTIONr_long_range_B_refined6.60916.1054613
X-RAY DIFFRACTIONr_long_range_B_other6.60916.1124614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 81 -
Rwork0.267 2650 -
obs--91.52 %
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)
14.6588-1.69911.39273.9226-0.50614.1382-0.0630.17910.41960.12690.0221-0.0873-0.3227-0.07410.04090.0510.01180.02020.02560.03620.0720.220958.98449.0705
25.0935-0.2403-0.41392.96030.06792.63160.0434-0.04880.48860.1712-0.02870.2987-0.2993-0.3476-0.01480.05050.04730.03050.06320.00510.0989-6.927355.500113.0805
32.1012-0.95120.56226.587-0.30612.732-0.04210.06140.01310.16280.2043-0.37390.13050.2607-0.16220.01240.0189-0.01730.0383-0.02580.03645.023842.517713.7069
42.1752-0.66280.69274.3417-0.85512.11810.02490.2801-0.1782-0.29290.02760.34520.0011-0.2428-0.05250.0777-0.005-0.04860.1511-0.0380.0682-11.410339.35361.8533
51.9242-0.73130.01393.02630.03792.19940.08490.3346-0.1232-0.46120.00440.02330.0312-0.0334-0.08930.0726-0.0113-0.00240.0842-0.02440.0122-2.866639.96043.2343
61.9281-0.55850.16284.90882.83966.9235-0.0663-0.2921-0.02690.29510.22270.35690.0699-0.1964-0.15640.02010.02440.02880.08270.04550.0599-9.173343.808419.0307
72.7361-0.51080.3084.52040.00466.3213-0.0394-0.1775-0.2382-0.1022-0.0058-0.16530.19160.17130.04520.13290.0266-0.01570.04090.06030.13195.985722.973328.2173
85.59850.4004-0.4744.3869-0.30213.4932-0.016-0.3251-0.41340.1212-0.00230.35150.4829-0.32270.01820.0972-0.02580.03070.09270.06080.0979-1.79426.696728.9122
93.31743.04050.09067.9244-0.02762.1948-0.07820.061-0.0189-0.11550.1488-0.1596-0.02290.1971-0.07050.02810.0157-0.00030.0550.01350.047.654139.535321.6086
102.8552-0.7326-0.07424.0935-0.55112.970.1075-0.5906-0.18470.408-0.01010.2172-0.0394-0.1124-0.09740.21320.0069-0.00640.2330.00090.03361.538242.680840.8854
113.73671.3966-0.37793.4088-0.0262.08690.0122-0.3872-0.20730.44870.1077-0.4193-0.00480.1555-0.120.08780.027-0.0470.1269-0.01360.06147.56342.035334.5955
124.01082.03972.40164.59632.62496.0411-0.0894-0.0967-0.17260.1160.16880.3779-0.072-0.5191-0.07940.01570.03190.03620.10590.0690.088-6.993738.494525.7713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 46
2X-RAY DIFFRACTION2A47 - 95
3X-RAY DIFFRACTION3A96 - 121
4X-RAY DIFFRACTION4B3 - 46
5X-RAY DIFFRACTION5B47 - 95
6X-RAY DIFFRACTION6B96 - 121
7X-RAY DIFFRACTION7C3 - 46
8X-RAY DIFFRACTION8C47 - 95
9X-RAY DIFFRACTION9C96 - 121
10X-RAY DIFFRACTION10D3 - 46
11X-RAY DIFFRACTION11D47 - 95
12X-RAY DIFFRACTION12D96 - 121

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