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- PDB-1nqn: Structure of Avm-W110K (W110K mutant of avidin) -

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Basic information

Entry
Database: PDB / ID: 1nqn
TitleStructure of Avm-W110K (W110K mutant of avidin)
ComponentsAvidin
KeywordsUNKNOWN FUNCTION / avidin / streptavidin / biotin / monomer-monomer interaction
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPazy, Y. / Eisenberg-Domovich, Y. / Laitinen, O.H. / Kulomaa, M.S. / Bayer, E.A. / Wilchek, M. / Livnah, O.
CitationJournal: J.Bacteriol. / Year: 2003
Title: Dimer-Tetramer Transition between Solution and Crystalline States of Streptavidin and Avidin Mutants.
Authors: Pazy, Y. / Eisenberg-Domovich, Y. / Laitinen, O.H. / Kulomaa, M.S. / Bayer, E.A. / Wilchek, M. / Livnah, O.
History
DepositionJan 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_database_remark / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_ref_seq_dif.details
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE According to Swiss-Prot entry P02701 there is a variant in residue 58 Ile -> Thr (IN APPR. ...SEQUENCE According to Swiss-Prot entry P02701 there is a variant in residue 58 Ile -> Thr (IN APPR. 50% OF THE CHAINS).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avidin
B: Avidin


Theoretical massNumber of molelcules
Total (without water)27,1552
Polymers27,1552
Non-polymers00
Water1,69394
1
A: Avidin
B: Avidin

A: Avidin
B: Avidin


Theoretical massNumber of molelcules
Total (without water)54,3094
Polymers54,3094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)67.703, 77.450, 42.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Avidin


Mass: 13577.255 Da / Num. of mol.: 2 / Mutation: W110K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVD / Cell line (production host): JM109 / Production host: Escherichia coli (E. coli) / References: UniProt: P02701
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 32% MPEG 2k, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
22.5 Msodium formate1reservoir
30.1 Macetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 21282 / % possible obs: 98.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 98 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / σ(F): 1
RfactorNum. reflection
Rfree0.227 -
Rwork0.205 -
all0.209 -
obs0.206 21282
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 94 1894
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.013
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.7

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