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- PDB-3exw: Crystal structure of the human Adenovirus type 7 fiber knob -

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Basic information

Entry
Database: PDB / ID: 3exw
TitleCrystal structure of the human Adenovirus type 7 fiber knob
ComponentsL5 fiber protein
KeywordsVIRAL PROTEIN / adenovirus / trimer / fiber knob / ad7 / ads
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
Fiber protein / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 7
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPersson, B.D. / Reiter, D.M. / Arnberg, N. / Stehle, T.
CitationJournal: J.Virol. / Year: 2009
Title: An arginine switch in the species B adenovirus knob determines high-affinity engagement of cellular receptor CD46
Authors: Persson, B.D. / Muller, S. / Reiter, D.M. / Schmitt, B.B. / Marttila, M. / Sumowski, C.V. / Schweizer, S. / Scheu, U. / Ochsenfeld, C. / Arnberg, N. / Stehle, T.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L5 fiber protein
B: L5 fiber protein
C: L5 fiber protein


Theoretical massNumber of molelcules
Total (without water)70,4683
Polymers70,4683
Non-polymers00
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-36 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.310, 88.050, 79.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein L5 fiber protein


Mass: 23489.217 Da / Num. of mol.: 3 / Fragment: residues 117-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Strain: Gomen / Gene: L5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q5EY45, UniProt: P15141*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 23% w/v PEG 3350, 0.1M HEPES buffer, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2006
RadiationMonochromator: Undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→79.06 Å / Num. all: 59433 / Num. obs: 52966 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rsym value: 0.05
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.34 / Rsym value: 0.364 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.3.0037refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Adenovirus type 11 fiber knob

Resolution: 1.75→36.11 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.906 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22999 5916 10 %RANDOM
Rwork0.19192 ---
obs0.19572 52966 99.08 %-
all-59433 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.948 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---1.03 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 0 492 5128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224743
X-RAY DIFFRACTIONr_bond_other_d0.0030.022957
X-RAY DIFFRACTIONr_angle_refined_deg0.7321.9326497
X-RAY DIFFRACTIONr_angle_other_deg0.65137281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.095601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47225.217207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44115739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721512
X-RAY DIFFRACTIONr_chiral_restr0.0540.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02944
X-RAY DIFFRACTIONr_nbd_refined0.2120.2871
X-RAY DIFFRACTIONr_nbd_other0.2180.23280
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22382
X-RAY DIFFRACTIONr_nbtor_other0.0840.22463
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2420
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.211
X-RAY DIFFRACTIONr_mcbond_it0.9831.53826
X-RAY DIFFRACTIONr_mcbond_other0.1731.51196
X-RAY DIFFRACTIONr_mcangle_it1.14424874
X-RAY DIFFRACTIONr_scbond_it1.69532096
X-RAY DIFFRACTIONr_scangle_it2.3654.51618
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2505 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.050.05
tight thermal0.170.5
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 441 -
Rwork0.278 3701 -
obs--94.5 %

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