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- PDB-1nob: KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 -

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Basic information

Entry
Database: PDB / ID: 1nob
TitleKNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12
ComponentsPROTEIN (FIBER KNOB PROTEIN)
KeywordsVIRAL PROTEIN / RECEPTOR BINDING
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 12
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M.
CitationJournal: Science / Year: 1999
Title: Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR.
Authors: Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M.
History
DepositionMay 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (FIBER KNOB PROTEIN)
C: PROTEIN (FIBER KNOB PROTEIN)
D: PROTEIN (FIBER KNOB PROTEIN)
E: PROTEIN (FIBER KNOB PROTEIN)
F: PROTEIN (FIBER KNOB PROTEIN)


Theoretical massNumber of molelcules
Total (without water)119,6676
Polymers119,6676
Non-polymers00
Water0
1
A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (FIBER KNOB PROTEIN)
C: PROTEIN (FIBER KNOB PROTEIN)


Theoretical massNumber of molelcules
Total (without water)59,8333
Polymers59,8333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-27 kcal/mol
Surface area20220 Å2
MethodPISA
2
D: PROTEIN (FIBER KNOB PROTEIN)
E: PROTEIN (FIBER KNOB PROTEIN)
F: PROTEIN (FIBER KNOB PROTEIN)


Theoretical massNumber of molelcules
Total (without water)59,8333
Polymers59,8333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-28 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.910, 104.820, 77.190
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.401223, -0.613278, 0.680375), (0.915832, -0.255212, 0.310031), (-0.016495, 0.7475, 0.664057)8.0953, -30.4701, 11.7403
2given(-0.4004, 0.915881, -0.029034), (-0.603457, -0.239707, 0.760513), (0.689579, 0.32203, 0.648673)31.6684, -12.0346, -3.2106
3given(0.999514, -0.017305, -0.02594), (0.027034, 0.895478, 0.444285), (0.015541, -0.44477, 0.89551)16.7759, -39.4777, 53.3371
4given(-0.397781, 0.837363, 0.374958), (-0.584753, -0.546307, 0.599678), (0.70699, 0.019283, 0.706961)-12.4872, 28.0182, 29.0256
5given(-0.380651, -0.844885, 0.375864), (0.924392, -0.358478, 0.130361), (0.024599, 0.397068, 0.91746)61.7458, 10.3491, 16.2028

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Components

#1: Protein
PROTEIN (FIBER KNOB PROTEIN)


Mass: 19944.477 Da / Num. of mol.: 6 / Fragment: KNOB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 12 / Genus: Mastadenovirus / Species: Human adenovirus A / Variant: SEROTYPE 12 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / Variant (production host): T7 / References: UniProt: P36711

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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 Å3/Da / Density % sol: 40 %
Crystal growpH: 7 / Details: 26% PEG 3350, pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
Conc.: 26 % / Common name: PEG3350

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: BRANDEIS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 27987 / % possible obs: 100 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.22 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNB

1knb


Resolution: 2.6→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1125 3.7 %SHELLS
Rwork0.24 ---
obs-30086 93 %-
Solvent computationBsol: 63 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1--3.26 Å20 Å24.405 Å2
2--2.027 Å20 Å2
3---1.236 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8406 0 0 0 8406
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM
Software
*PLUS
Name: CNS / Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 3.7 % / Rfactor obs: 0.241 / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.7

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