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- PDB-1p2z: Refinement of Adenovirus Type 2 Hexon with CNS -

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Basic information

Entry
Database: PDB / ID: 1p2z
TitleRefinement of Adenovirus Type 2 Hexon with CNS
ComponentsHexon protein
KeywordsVIRAL PROTEIN / ADENOVIRUS / TYPE 2 / HEXON / VIRUS / JELLYROLL / COAT PROTEIN
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Hexon Major Viral Coat Protein; domain 3 / Hexon Major Viral Coat Protein, domain 3 / Hexon Major Viral Coat Protein; domain 2 / Hexon Major Viral Coat Protein, domain 2 / Adenovirus Type 2 Hexon; domain 1 / Adenovirus Type 2 Hexon, domain 1 / Adenovirus Type 2 Hexon, domain 4 / Adenovirus Type 2 Hexon; domain 4 / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal ...Hexon Major Viral Coat Protein; domain 3 / Hexon Major Viral Coat Protein, domain 3 / Hexon Major Viral Coat Protein; domain 2 / Hexon Major Viral Coat Protein, domain 2 / Adenovirus Type 2 Hexon; domain 1 / Adenovirus Type 2 Hexon, domain 1 / Adenovirus Type 2 Hexon, domain 4 / Adenovirus Type 2 Hexon; domain 4 / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein / Beta Complex / Distorted Sandwich / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRux, J.J. / Kuser, P.R. / Burnett, R.M.
Citation
Journal: J.VIROL. / Year: 2003
Title: Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution x-ray crystallographic, molecular modeling, and sequence-based methods
Authors: Rux, J.J. / Kuser, P.R. / Burnett, R.M.
#1: Journal: MOL.THER. / Year: 2000
Title: Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon.
Authors: Rux, J.J. / Burnett, R.M.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: The refined crystal structure of hexon, the major coat protein of adenovirus type 2, at 2.9 A resolution.
Authors: Athappilly, F.K. / Murali, R. / Rux, J.J. / Cai, Z. / Burnett, R.M.
#3: Journal: ADENOVIRUS METHODS AND PROTOCOLS (IN: METHODS IN MOLECULAR MEDICINE, V.21)
Year: 1999
Title: Large-scale purification and crystallization of adenovirus hexon
Authors: Rux, J.J. / Pascolini, D. / Burnett, R.M.
History
DepositionApr 16, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionNov 11, 2003ID: 1DHX
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE PROTEIN IS ACETYLATED AT THE N-TERMINUS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0826
Polymers109,1211
Non-polymers9615
Water7,746430
1
A: Hexon protein
hetero molecules

A: Hexon protein
hetero molecules

A: Hexon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,24518
Polymers327,3633
Non-polymers2,88215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area54000 Å2
ΔGint-271 kcal/mol
Surface area81600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)150.540, 150.540, 150.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-971-

CIT

21A-971-

CIT

DetailsThe biological assembly is a trimer generated by the operations z, x, y and y, z, x.

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Components

#1: Protein Hexon protein / Late protein 2


Mass: 109121.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 2 / Genus: Mastadenovirus / Species: Human adenovirus C / References: UniProt: P03277
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.2
Details: 0.5 M SODIUM CITRATE , pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Apr 1, 1991 / Details: MIRRORS
RadiationMonochromator: double-mirror focusing system (Supper) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. all: 57118 / Num. obs: 48199 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 5.6 Å2 / Rsym value: 0.098
Reflection shellResolution: 2.2→2.32 Å / Num. unique all: 7162 / % possible all: 75.8

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Processing

Software
NameVersionClassification
CNS0.9refinement
XDSdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RUX

1rux
PDB Unreleased entry


Resolution: 2.2→9.99 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2422 5 %RANDOM
Rwork0.178 ---
obs0.178 48199 84.4 %-
all-57118 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.9291 Å2 / ksol: 0.399606 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6914 0 65 430 7409
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it0.951.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.432
X-RAY DIFFRACTIONc_scangle_it2.112.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 368 5.1 %
Rwork0.266 6794 -
obs-7162 75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIT.PARAMCIT.TOP

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