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- PDB-1knb: CRYSTAL STRUCTURE OF THE RECEPTOR-BINDING DOMAIN OF ADENOVIRUS TY... -

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Basic information

Entry
Database: PDB / ID: 1knb
TitleCRYSTAL STRUCTURE OF THE RECEPTOR-BINDING DOMAIN OF ADENOVIRUS TYPE 5 FIBER PROTEIN AT 1.7 ANGSTROMS RESOLUTION
ComponentsADENOVIRUS TYPE 5 FIBER PROTEIN
KeywordsCELL RECEPTOR RECOGNITION
Function / homology
Function and homology information


viral capsid, fiber / adhesion receptor-mediated virion attachment to host cell / 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 5
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsXia, D. / Henry, L.J. / Gerard, R.D. / Deisenhofer, J.
Citation
Journal: Structure / Year: 1994
Title: Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 A resolution.
Authors: Xia, D. / Henry, L.J. / Gerard, R.D. / Deisenhofer, J.
#1: Journal: J.Virol. / Year: 1994
Title: Characterization of the Knob Domain of the Adenovirus Type 5 Fiber Protein Expressed in Escherichia Coli
Authors: Henry, L.J. / Xia, D. / Wilke, M.E. / Deisenhofer, J. / Gerard, R.D.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Structure of Adenovirus Fiber: Morphology of Single Fibers
Authors: Ruigrok, R.W.H. / Barge, A. / Albiges-Rizo, C. / Dayan, S.
History
DepositionJan 6, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENOVIRUS TYPE 5 FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2571
Polymers21,2571
Non-polymers00
Water2,612145
1
A: ADENOVIRUS TYPE 5 FIBER PROTEIN

A: ADENOVIRUS TYPE 5 FIBER PROTEIN

A: ADENOVIRUS TYPE 5 FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)63,7703
Polymers63,7703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Unit cell
Length a, b, c (Å)86.400, 86.400, 86.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Atom site foot note1: CIS PROLINE - PRO 447

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Components

#1: Protein ADENOVIRUS TYPE 5 FIBER PROTEIN


Mass: 21256.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 5 / Genus: Mastadenovirus / Species: Human adenovirus C / Production host: Escherichia coli (E. coli) / References: UniProt: P11818
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
22 %(v/v)PEG4001drop
330 %ammonium sulphate1drop
40.1 Mimidazol1drop
52 %(v/v)PEG4001reservoir
630 %ammonium sulphate1reservoir
70.1 Mimidazol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→12 Å / Num. obs: 17633 / % possible obs: 73.9 % / Observed criterion σ(I): 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.158 / Rfactor obs: 0.158 / Highest resolution: 1.7 Å
Details: IN THE MONOMER STRUCTURE, THERE ARE TWO REGIONS WHERE B FACTORS ARE HIGH. ONE REGION IS FROM 396 - 397 WHICH IS LOCATED AT THE N-TERMINUS. THE OTHER REGION IS BETWEEN BETA STRANDS H AND I FOR RESIDUES 540 - 546.
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 0 435 2177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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