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- PDB-2a5b: Avidin complexed with 8-oxodeoxyguanosine -

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Basic information

Entry
Database: PDB / ID: 2a5b
TitleAvidin complexed with 8-oxodeoxyguanosine
ComponentsAvidin
KeywordsUNKNOWN FUNCTION / Avidin / Damaged DNA / 8-oxodeoxyguanosine
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
2'-DEOXY-8-OXOGUANOSINE / Avidin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsConners, R. / Hooley, E. / Thomas, S. / Brady, R.L.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Recognition of oxidatively modified bases within the biotin-binding site of avidin.
Authors: Conners, R. / Hooley, E. / Clarke, A.R. / Thomas, S. / Brady, R.L.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id

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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)28,4515
Polymers27,7252
Non-polymers7263
Water79344
1
A: Avidin
B: Avidin
hetero molecules

A: Avidin
B: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,90210
Polymers55,4504
Non-polymers1,4516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area12310 Å2
ΔGint-23 kcal/mol
Surface area22370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.019, 79.487, 42.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
12A
22B

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSTHRTHRAA4 - 344 - 34
211CYSCYSTHRTHRBB4 - 344 - 34
321SERSERLYSLYSAA47 - 5847 - 58
421SERSERLYSLYSBB47 - 5847 - 58
531THRTHRCYSCYSAA63 - 8363 - 83
631THRTHRCYSCYSBB63 - 8363 - 83
741GLUGLUVALVALAA91 - 10391 - 103
841GLUGLUVALVALBB91 - 10391 - 103
951TRPTRPPHEPHEAA110 - 120110 - 120
1051TRPTRPPHEPHEBB110 - 120110 - 120
112NAGNAGNAGNAGAC201
212NAGNAGNAGNAGBE201

NCS ensembles :
ID
1
2

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Components

#1: Protein Avidin


Mass: 13862.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02701
#2: 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.: 2
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
#3: Chemical ChemComp-8HG / 2'-DEOXY-8-OXOGUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9795 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 18, 2004
RadiationMonochromator: Si 111 Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→52.7 Å / Num. all: 8683 / Num. obs: 8270 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 23.5
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.41 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJ8

1ij8


Resolution: 2.49→52.7 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.842 / SU B: 10.983 / SU ML: 0.25 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.296 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31007 413 4.8 %RANDOM
Rwork0.21905 ---
obs0.22331 8270 98.49 %-
all-8683 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.168 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å20 Å2
2---1.56 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.49→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 48 44 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211974
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.942689
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7555246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90123.88285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3151513
X-RAY DIFFRACTIONr_chiral_restr0.1240.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021484
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2783
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21312
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0350.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.211.51243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0721960
X-RAY DIFFRACTIONr_scbond_it2.4623862
X-RAY DIFFRACTIONr_scangle_it3.9434.5729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1352tight positional0.070.05
1312loose positional0.245
214loose positional0.35
1352tight thermal0.290.5
1312loose thermal2.1410
214loose thermal5.310
LS refinement shellResolution: 2.49→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 31 -
Rwork0.34 565 -
obs--95.51 %

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