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- PDB-2bzv: Human Enteric Adenovirus Serotype 41 Short Fiber Head (pH8) -

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Basic information

Entry
Database: PDB / ID: 2bzv
TitleHuman Enteric Adenovirus Serotype 41 Short Fiber Head (pH8)
ComponentsFIBER PROTEIN 2
KeywordsVIRAL PROTEIN / ADENOVIRUS / FIBER / RECEPTOR / AD41 / FIBER PROTEIN
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, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / 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
Biological speciesHUMAN ADENOVIRUS TYPE 41
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsSeiradake, E. / Cusack, S.
CitationJournal: J.Virol. / Year: 2005
Title: Crystal Structure of Enteric Adenovirus Serotype 41 Short Fiber Head.
Authors: Seiradake, E. / Cusack, S.
History
DepositionAug 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBER PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)20,1491
Polymers20,1491
Non-polymers00
Water5,999333
1
A: FIBER PROTEIN 2

A: FIBER PROTEIN 2

A: FIBER PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)60,4463
Polymers60,4463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
MethodPQS
Unit cell
Length a, b, c (Å)103.730, 103.730, 103.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-2285-

HOH

21A-2286-

HOH

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Components

#1: Protein FIBER PROTEIN 2 / HUMAN ADENOVIRUS SEROTYPE 41 SHORT FIBER HEAD


Mass: 20148.709 Da / Num. of mol.: 1 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 215-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN ADENOVIRUS TYPE 41 / Plasmid: PPROEX-HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P16883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRECOGNIZES THE CELL RECEPTOR
Sequence detailsC-TERMINAL FRAGMENT (RESIDUES 215-387) WITH C-TERMINAL HIS- TAG

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 8
Details: 20% PEG3350, 0.25 M SODIUM DIHYDROGEN PHOSPHATE MONOBASIC, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.15→100 Å / Num. obs: 351024 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BZU

2bzu


Resolution: 1.15→30 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.692 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.131 3183 5.1 %RANDOM
Rwork0.124 ---
obs0.124 58983 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.32 Å2
Refinement stepCycle: LAST / Resolution: 1.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 0 333 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221256
X-RAY DIFFRACTIONr_bond_other_d0.0020.021093
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9391739
X-RAY DIFFRACTIONr_angle_other_deg1.1832582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16825.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1115205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.666153
X-RAY DIFFRACTIONr_chiral_restr0.0860.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021426
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02250
X-RAY DIFFRACTIONr_nbd_refined0.3790.2248
X-RAY DIFFRACTIONr_nbd_other0.2570.21093
X-RAY DIFFRACTIONr_nbtor_refined0.210.2617
X-RAY DIFFRACTIONr_nbtor_other0.0880.2638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0071.5796
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.86321279
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5913530
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7774.5445
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.184 252
Rwork0.178 4320

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