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- PDB-7p4z: Crystal structure of avidin from hen egg white in space group C2 -

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Basic information

Entry
Database: PDB / ID: 7p4z
TitleCrystal structure of avidin from hen egg white in space group C2
ComponentsAvidin
KeywordsANTIMICROBIAL PROTEIN / avidin / gallus
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBellini, D. / Gorrec, F.
CitationJournal: J.Appl.Crystallogr. / Year: 2022
Title: The FUSION protein crystallization screen.
Authors: Gorrec, F. / Bellini, D.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)27,4194
Polymers26,9762
Non-polymers4422
Water23413
1
A: Avidin
B: Avidin
hetero molecules

A: Avidin
B: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8378
Polymers53,9534
Non-polymers8854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11120 Å2
ΔGint-31 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.424, 43.304, 62.314
Angle α, β, γ (deg.)90.000, 109.044, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: Protein Avidin


Mass: 13488.159 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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: obtained synthetically / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M MES/Imidazole pH 6.5, 0.4% of each Anaesthetic alkaloid (Morpheus Fusion screen, well H12)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→58.92 Å / Num. obs: 14917 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 34.57 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 6 / Rpim(I) all: 3 / Rrim(I) all: 4.9 / Net I/σ(I): 15.5
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 9.9 / Num. unique obs: 695 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y53

1y53


Resolution: 2.2→58.9 Å / SU ML: 0.2569 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 36.3499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2906 789 5.32 %
Rwork0.247 14046 -
obs0.2493 14835 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 0 13 1870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751891
X-RAY DIFFRACTIONf_angle_d1.21292555
X-RAY DIFFRACTIONf_chiral_restr0.1309297
X-RAY DIFFRACTIONf_plane_restr0.0095317
X-RAY DIFFRACTIONf_dihedral_angle_d6.9698254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.31371240.29222278X-RAY DIFFRACTION97.4
2.34-2.520.36631190.28962322X-RAY DIFFRACTION99.23
2.52-2.770.33991450.27822318X-RAY DIFFRACTION99.43
2.77-3.170.28171250.26552354X-RAY DIFFRACTION99.68
3.17-3.990.30491410.23972354X-RAY DIFFRACTION99.8
4-58.90.25311350.21952420X-RAY DIFFRACTION99.69

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