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- PDB-4v86: Structure-function Analysis of Receptor-binding in Adeno-Associat... -

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Basic information

Entry
Database: PDB / ID: 4v86
TitleStructure-function Analysis of Receptor-binding in Adeno-Associated Virus Serotype 6 (AAV-6)
ComponentsCapsid protein VP1
KeywordsVIRUS / beta barrel
Function / homologyPhospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein VP1
Function and homology information
Biological speciesAdeno-associated virus - 6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.003 Å
AuthorsXie, Q.
CitationJournal: Virology / Year: 2011
Title: Structure-function analysis of receptor-binding in adeno-associated virus serotype 6 (AAV-6).
Authors: Xie, Q. / Lerch, T.F. / Meyer, N.L. / Chapman, M.S.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3TSX, 1VU0, 1VU1
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
U: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
a: Capsid protein VP1
b: Capsid protein VP1
c: Capsid protein VP1
d: Capsid protein VP1
e: Capsid protein VP1
f: Capsid protein VP1
g: Capsid protein VP1
h: Capsid protein VP1
i: Capsid protein VP1
j: Capsid protein VP1
k: Capsid protein VP1
l: Capsid protein VP1
m: Capsid protein VP1
n: Capsid protein VP1
o: Capsid protein VP1
p: Capsid protein VP1
q: Capsid protein VP1
r: Capsid protein VP1
s: Capsid protein VP1
t: Capsid protein VP1
u: Capsid protein VP1
v: Capsid protein VP1
w: Capsid protein VP1
x: Capsid protein VP1
y: Capsid protein VP1
z: Capsid protein VP1
0: Capsid protein VP1
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
7: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)3,501,63660
Polymers3,501,63660
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)354.793, 363.897, 371.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ...
Capsid protein VP1 /


Mass: 58360.598 Da / Num. of mol.: 60 / Fragment: UNP residues 217-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 6 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: O56137

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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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 4-6% PEG6000, 100 mM HEPES, 50 mM magnesium chloride,, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 1, 2004
RadiationMonochromator: Single-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 3.003→49.21 Å / Num. all: 332221 / Num. obs: 332221 / % possible obs: 42 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 3.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
GLRFphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.003→49.21 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.96 / σ(F): 0 / Phase error: 31.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2862 3268 0.98 %
Rwork0.251 --
obs0.2513 332221 35.15 %
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.443 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 149.19 Å2 / Biso mean: 62.7664 Å2 / Biso min: 35.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.3052 Å2-0 Å20 Å2
2---14.6931 Å20 Å2
3---17.0997 Å2
Refinement stepCycle: LAST / Resolution: 3.003→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms82420 0 0 0 82420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012254820
X-RAY DIFFRACTIONf_angle_d1.203347520
X-RAY DIFFRACTIONf_chiral_restr0.07436240
X-RAY DIFFRACTIONf_plane_restr0.00646020
X-RAY DIFFRACTIONf_dihedral_angle_d15.97391320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.003-3.30510.39086090.4001622346284327
3.3051-3.78320.35668120.3244843348514636
3.7832-4.76580.28749600.2374955519651141
4.7658-49.21690.2218870.1821868348772137

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