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- PDB-3ng9: Structure to Function Correlations for Adeno-associated Virus Ser... -

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Basic information

Entry
Database: PDB / ID: 3ng9
TitleStructure to Function Correlations for Adeno-associated Virus Serotype 1
ComponentsCapsid protein
KeywordsVIRUS / Adeno-Associated Virus 1 / beta barrel / single-stranded DNA virus / parvovirus / icosahedral virus
Function / homology
Function and homology information


T=1 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
ADENINE / 6-AMINOPYRIMIDIN-2(1H)-ONE / Capsid protein
Similarity search - Component
Biological speciesAdeno-associated virus - 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGovindasamy, L. / Miller, E.B. / Gurda, B. / McKenna, R. / Zolotukhin, S. / Muzyczka, N. / Agbandje-McKenna, M.
CitationJournal: To be Published
Title: Structure to Function Correlations for Adeno-Associated Virus serotype 1
Authors: Govindasamy, L. / Miller, E.B. / Gurda, B. / McKenna, R. / Zolotukhin, S. / Muzyczka, N. / Agbandje-McKenna, M.
History
DepositionJun 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)817,01230
Polymers814,54910
Non-polymers2,46220
Water23,4201300
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)4,902,069180
Polymers4,887,29560
Non-polymers14,774120
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
hetero molecules


  • crystal asymmetric unit, crystal frame
  • 817 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)817,01230
Polymers814,54910
Non-polymers2,46220
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Unit cell
Length a, b, c (Å)262.700, 262.700, 612.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Components on special symmetry positions
IDModelComponents
11J-871-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

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Components

#1: Protein
Capsid protein


Mass: 81454.922 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 1 / References: UniProt: Q9WBP8
#2: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical
ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H5N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1300 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 1.0 M NaCl and 7% PEG 6K, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 247785 / % possible obs: 89 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.129 / Rsym value: 0.123 / Net I/σ(I): 12.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.3 / Num. unique all: 13401 / Rsym value: 0.206 / % possible all: 48.6

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Processing

Software
NameVersionClassification
MAR345data collection
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G8G

2g8g


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.324 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25 12421 5 %RANDOM
Rwork0.23 ---
obs0.23 235361 89.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.488 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å2-1.61 Å20 Å2
2---3.22 Å20 Å2
3---4.82 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41200 0 180 1300 42680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02242650
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.92958150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.66255190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97124.3192130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.769156350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.35915210
X-RAY DIFFRACTIONr_chiral_restr0.1430.26020
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02133950
X-RAY DIFFRACTIONr_mcbond_it1.051.525970
X-RAY DIFFRACTIONr_mcangle_it2.061242070
X-RAY DIFFRACTIONr_scbond_it3.124316680
X-RAY DIFFRACTIONr_scangle_it4.8694.516080
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4260 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.050.05
Btight positional0.050.05
Ctight positional0.060.05
Dtight positional0.050.05
Etight positional0.050.05
Ftight positional0.060.05
Gtight positional0.050.05
Htight positional0.050.05
Itight positional0.060.05
Jtight positional0.060.05
Atight thermal0.140.5
Btight thermal0.140.5
Ctight thermal0.130.5
Dtight thermal0.130.5
Etight thermal0.140.5
Ftight thermal0.150.5
Gtight thermal0.150.5
Htight thermal0.140.5
Itight thermal0.140.5
Jtight thermal0.160.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 446 -
Rwork0.341 8931 -
obs--45.99 %

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