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- PDB-1uxe: ADENOVIRUS AD37 FIBRE HEAD -

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Basic information

Entry
Database: PDB / ID: 1uxe
TitleADENOVIRUS AD37 FIBRE HEAD
ComponentsFIBER PROTEIN
KeywordsVIRAL PROTEIN / ADENOVIRUS / AD37 / 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 / 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 37
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)65,4648
Polymers65,1503
Non-polymers3145
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.490, 70.360, 75.280
Angle α, β, γ (deg.)90.00, 94.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.099, 0.9406, -0.3247), (0.2141, 0.3387, 0.9162), (0.9718, 0.0212, -0.2349)34.022, -38.115, 25.799
2given(-0.1029), (), ()-13.208, -20.061, 51.858

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Components

#1: Protein FIBER PROTEIN


Mass: 21716.535 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 37 / Strain: P / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64823
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAINS A-C, TYR 173 TO ALA 173 ENGINEERED MUTATION IN CHAINS A-C, LEU 174 TO ...ENGINEERED MUTATION IN CHAINS A-C, TYR 173 TO ALA 173 ENGINEERED MUTATION IN CHAINS A-C, LEU 174 TO MET 174 ENGINEERED MUTATION IN CHAINS A-C, VAL 175 TO GLY 175 ENGINEERED MUTATION IN CHAINS A-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 % / Description: ISOMORPHOUS
Crystal growpH: 7.5
Details: RESERVOIR: 24 % PEG8000, 50 MM ZINC ACETATE, 100 MM HEPES, PH 7.5 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: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 9, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→51.3 Å / Num. obs: 42295 / % possible obs: 98.2 % / Redundancy: 3.58 % / Biso Wilson estimate: 24.51 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 4.177
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.45 / % possible all: 96.9

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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: 2→51.3 Å / Rfactor Rfree error: 0.005 / 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
Rfree0.241 2170 5 %RANDOM
Rwork0.204 ---
obs0.204 42597 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.04 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 27.13 Å2
Baniso -1Baniso -2Baniso -3
1--4.833 Å20 Å2-3.057 Å2
2---0.307 Å20 Å2
3---5.139 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 11 385 4745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0228
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.97
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.5593.5
X-RAY DIFFRACTIONc_mcangle_it3.3624
X-RAY DIFFRACTIONc_scbond_it3.3534
X-RAY DIFFRACTIONc_scangle_it4.4614.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.309 210 5.6 %
Rwork0.286 3718 -
obs--89.74 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.TOP

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