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- PDB-1uxb: ADENOVIRUS AD19p FIBRE HEAD in complex with sialyl-lactose -

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Basic information

Entry
Database: PDB / ID: 1uxb
TitleADENOVIRUS AD19p FIBRE HEAD in complex with sialyl-lactose
ComponentsFIBER PROTEIN
KeywordsVIRAL PROTEIN / ADENOVIRUS / AD19P / FIBRE / RECEPTOR / SIALIC ACID / NEURAMINIC ACID / CD46 / DAF / CONJUNCTIVITIS
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 / nucleus / metal ion binding
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 19
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBurmeister, W.P. / Guilligay, D. / Cusack, S. / Wadell, G. / Arnberg, N.
CitationJournal: J.Virol. / Year: 2004
Title: Crystal Structure of Species D Adenovirus Fiber Knobs and Their Sialic Acid Binding Sites
Authors: Burmeister, W.P. / Guilligay, D. / Cusack, S. / Wadell, G. / Arnberg, N.
History
DepositionFeb 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,94012
Polymers65,1523
Non-polymers1,7889
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.700, 68.700, 74.700
Angle α, β, γ (deg.)90.00, 94.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0916, 0.9494, -0.3005), (0.2103, 0.3134, 0.9261), (0.9733, 0.0216, -0.2284)29.119, -36.852, 27.198
2given(-0.1, 0.1965, 0.9754), (0.9463, 0.3215, 0.0322), (-0.3073, 0.9263, -0.2181)15.212, -17.781, 48.275

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein FIBER PROTEIN


Mass: 21717.455 Da / Num. of mol.: 3 / Fragment: HEAD DOMAIN, RESIDUES 172-365 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ONLY THE KNOB DOMAIN, AFTER TEV CLEAVAGE OF A HIS-TAGGED PROTEIN CONSTRUCT
Source: (gene. exp.) HUMAN ADENOVIRUS TYPE 19 / Strain: P / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64822

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Sugars , 2 types, 3 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 593 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION IN CHAINS A, B, C, TYR 173 TO ALA 173 ENGINEERED MUTATION IN CHAINS A, B, C, ...ENGINEERED MUTATION IN CHAINS A, B, C, TYR 173 TO ALA 173 ENGINEERED MUTATION IN CHAINS A, B, C, LEU 174 TO MET 174 ENGINEERED MUTATION IN CHAINS A, B, C, VAL 175 TO GLY 175 ENGINEERED MUTATION IN CHAINS A, B, C, ALA 176 TO SER 176
Sequence detailsTHE FIRST FIVE RESIDUES HAVE BEEN CHANGED IN ORDER TO INTRODUCE THE TEV CLEAVAGE SITE

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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: 2.43 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5
Details: RESERVOIR: 24 % PEG8000, 50 MM ZINC ACETATE, 100 MM HEPES. PROTEIN: 30 MM TRIS-HCL, PH 7.5, 150 MM NACL.

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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 / Date: Jul 8, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→74.54 Å / Num. obs: 62060 / % possible obs: 100 % / Redundancy: 4.34 % / Biso Wilson estimate: 23.36 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 3.2063
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.39 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UXA

1uxa


Resolution: 1.75→74.54 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ELECTRON DENSITY THAT IS ASSOCIATED WITH THE ACETATE IONS IS POORLY DEFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3078 5 %RANDOM
Rwork0.175 ---
obs0.175 61498 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.96 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 26.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.997 Å20 Å2-0.639 Å2
2---1.077 Å20 Å2
3---2.074 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.75→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 111 587 5047
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0162
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_deg1.894
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.71
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.3173.5
X-RAY DIFFRACTIONc_mcangle_it4.0354
X-RAY DIFFRACTIONc_scbond_it4.4074
X-RAY DIFFRACTIONc_scangle_it5.9494.5
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.31 294 5.3 %
Rwork0.2678 5558 -
obs--94.91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.TOP

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