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- PDB-1qhv: HUMAN ADENOVIRUS SEROTYPE 2 FIBRE HEAD -

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Basic information

Entry
Database: PDB / ID: 1qhv
TitleHUMAN ADENOVIRUS SEROTYPE 2 FIBRE HEAD
ComponentsPROTEIN (ADENOVIRUS FIBRE)
KeywordsVIRAL PROTEIN / RECEPTOR BINDING / EXTRA-ORDINARY STABILITY
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fiber protein / Adenovirus type 2 partial fiber gene with mutation sites H2 ts 125
Similarity search - Component
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsVan Raaij, M.J. / Louis, N. / Chroboczek, J. / Cusack, S.
Citation
Journal: Virology / Year: 1999
Title: Structure of the human adenovirus serotype 2 fiber head domain at 1.5 A resolution.
Authors: van Raaij, M.J. / Louis, N. / Chroboczek, J. / Cusack, S.
#1: Journal: J.Virol. / Year: 1994
Title: Cell-Binding Domain of Adenovirus Serotype 2 Fiber
Authors: Louis, N. / Fender, P. / Barge, A. / Kitts, P. / Chroboczek, J.
History
DepositionMay 28, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ADENOVIRUS FIBRE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6713
Polymers21,4791
Non-polymers1922
Water5,495305
1
A: PROTEIN (ADENOVIRUS FIBRE)
hetero molecules

A: PROTEIN (ADENOVIRUS FIBRE)
hetero molecules

A: PROTEIN (ADENOVIRUS FIBRE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0139
Polymers64,4373
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9510 Å2
ΔGint-110 kcal/mol
Surface area22340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.350, 95.350, 48.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-303-

HOH

31A-304-

HOH

41A-305-

HOH

51A-306-

HOH

DetailsTHE FUNCTIONAL MOLECULE IS A TRIMER. THIS TRIMER IS GENERATED USING THE THREE-FOLD AXIS SYMMETRY.

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Components

#1: Protein PROTEIN (ADENOVIRUS FIBRE)


Mass: 21478.893 Da / Num. of mol.: 1 / Fragment: HEAD DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 2 / Genus: Mastadenovirus / Species: Human adenovirus C / Strain: SEROTYPE 2 / Gene: LOCUS AD2H2 / Plasmid: PACCL29 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q96590, UniProt: P03275*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58 %
Crystal growpH: 4
Details: 100 MM SODIUM ACETATE 25 % (V/V) GLYCEROL 1-1.5 M AMMONIUM SULPHATE PH 4.0 WITH ACETIC ACID
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / PH range low: 5.2 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0-1.5 Mammonium sulfate1reservoir
20.1 Msodium sulfate1reservoir
30.1 Msodium acetate1reservoir
425 %(v/v)glycerol1reservoir
520 mg/mlprotain1drop
61 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.993
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 1.51→10.97 Å / Num. obs: 36820 / % possible obs: 91.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.073 / Net I/σ(I): 7.3
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.172 / % possible all: 55.3
Reflection
*PLUS
Num. measured all: 386827 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 55.3 % / Num. unique obs: 3170 / Rmerge(I) obs: 0.172

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KNB

1knb


Resolution: 1.51→10.97 Å / SU B: 0.80142 / SU ML: 0.02897 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05292 / ESU R Free: 0.05087
RfactorNum. reflection% reflectionSelection details
Rfree0.143 1119 3 %RANDOM
Rwork0.109 ---
obs-35701 91.8 %-
Displacement parametersBiso mean: 23.07 Å2
Refinement stepCycle: LAST / Resolution: 1.51→10.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 10 305 1823
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0140.01
X-RAY DIFFRACTIONp_planar_d0.0150.017
X-RAY DIFFRACTIONp_hb_or_metal_coord0.02
X-RAY DIFFRACTIONp_mcbond_it5.8463
X-RAY DIFFRACTIONp_mcangle_it6.8925
X-RAY DIFFRACTIONp_scbond_it9.2083
X-RAY DIFFRACTIONp_scangle_it10.8645
X-RAY DIFFRACTIONp_plane_restr0.02640.03
X-RAY DIFFRACTIONp_chiral_restr0.1050.07
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1120.3
X-RAY DIFFRACTIONp_planar_tor4.91.5
X-RAY DIFFRACTIONp_staggered_tor11.615
X-RAY DIFFRACTIONp_transverse_tor30.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 3 % / Rfactor obs: 0.109
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.01
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.07
LS refinement shell
*PLUS
Rfactor Rfree: 0.18 / Rfactor obs: 0.136

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