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- PDB-2wt1: Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre... -

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Basic information

Entry
Database: PDB / ID: 2wt1
TitleGalectin domain of porcine adenovirus type 4 NADC-1 isolate fibre complexed with lacto-N-neo-tetraose
ComponentsPUTATIVE FIBER PROTEIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


galactoside binding / viral capsid / carbohydrate binding / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenovirus fibre protein / Adenovirus pIV-like, attachment domain / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. ...Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenovirus fibre protein / Adenovirus pIV-like, attachment domain / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / Galectin domain-containing protein
Similarity search - Component
Biological speciesPORCINE ADENOVIRUS 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGuardado-Calvo, P. / Munoz, E.M. / Llamas-Saiz, A.L. / Fox, G.C. / Glasgow, J.N. / van Raaij, M.J.
Citation
Journal: J. Virol. / Year: 2010
Title: Crystallographic structure of porcine adenovirus type 4 fiber head and galectin domains.
Authors: Guardado-Calvo, P. / Munoz, E.M. / Llamas-Saiz, A.L. / Fox, G.C. / Kahn, R. / Curiel, D.T. / Glasgow, J.N. / van Raaij, M.J.
#1: Journal: Virus Res. / Year: 1995
Title: Sequence Analysis of the Fiber Genomic Region of a Porcine Adenovirus Predicts a Novel Fiber Protein.
Authors: Kleiboeker, S.B.
#2: Journal: Cancer Biol.Ther. / Year: 2008
Title: Characterization of Infectivity of Knob-Modified Adenoviral Vectors in Glioma.
Authors: Paul, C.P.L. / Everts, M. / Glasgow, J.N. / Dent, P. / Fisher, P.B. / Ulasov, I.V. / Lesniak, M.S. / Stoff-Khalili, M.A. / Roth, J.C. / Preuss, M.A. / Dirven, C.M.F. / Lamfers, M.L.M. / ...Authors: Paul, C.P.L. / Everts, M. / Glasgow, J.N. / Dent, P. / Fisher, P.B. / Ulasov, I.V. / Lesniak, M.S. / Stoff-Khalili, M.A. / Roth, J.C. / Preuss, M.A. / Dirven, C.M.F. / Lamfers, M.L.M. / Siegal, G.P. / Zhu, Z.B. / Curiel, D.T.
#3: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2009
Title: Crystallization of the head and galectin-like domains of porcine adenovirus isolate NADC-1 fibre.
Authors: Guardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / Glasgow, J.N. / van Raaij, M.J.
History
DepositionSep 10, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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

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Assembly

Deposited unit
A: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8035
Polymers37,9091
Non-polymers8944
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.420, 38.790, 84.400
Angle α, β, γ (deg.)90.00, 102.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PUTATIVE FIBER PROTEIN


Mass: 37909.156 Da / Num. of mol.: 1 / Fragment: GALECTIN DOMAIN, RESIDUES 393-703
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PORCINE ADENOVIRUS 4 / Variant: NADC-1 ISOLATE / Plasmid: PET28C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83467
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-2/a4-b1_b3-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBETA-D-GALACTOSE (GAL): PART OF OLIGOMER ALPHA-D-GLUCOSE (BGC): PART OF OLIGOMER N-ACETYL-D- ...BETA-D-GALACTOSE (GAL): PART OF OLIGOMER ALPHA-D-GLUCOSE (BGC): PART OF OLIGOMER N-ACETYL-D-GLUCOSAMINE (NAG): PART OF OLIGOMER

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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: 39 % / Description: NONE
Crystal growpH: 8
Details: 10 MM TRIS-HCL PH 8.0, 27% (W/V) POLY -ETHYLENE GLYCOL 3350, 200 MM LITHIUM NITRATE 5 MM DITHIOTHREITOL, 5 MM LACTO-N-NEO-TETRAOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: CCD / Date: May 26, 2009
Details: TWO CYLINDRICAL VERTICAL FOCUSING PARABOLIC MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI (111), SI(311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 23751 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WSU CHAIN A

2wsu


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.434 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22296 1213 5.1 %RANDOM
Rwork0.18759 ---
obs0.1894 22538 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å2-1.35 Å2
2---0.27 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 60 145 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222473
X-RAY DIFFRACTIONr_bond_other_d0.0010.021653
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9983385
X-RAY DIFFRACTIONr_angle_other_deg0.82934037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26823.868106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8031514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
X-RAY DIFFRACTIONr_nbd_refined0.2060.02366
X-RAY DIFFRACTIONr_nbd_other0.2010.021632
X-RAY DIFFRACTIONr_nbtor_refined0.1760.021176
X-RAY DIFFRACTIONr_nbtor_other0.0860.021350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.02130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.0213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.0240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.0211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2151509
X-RAY DIFFRACTIONr_mcbond_other0.8155591
X-RAY DIFFRACTIONr_mcangle_it3.10672461
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4547964
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.769924
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→2.003 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.31 153 -
Rwork0.275 2995 -
obs--90.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
122.5110.1677-13.141531.1991-6.120913.3711-0.3538-0.9811.52440.15291.1212-0.9306-0.58490.6733-0.76730.3993-0.0965-0.05820.4049-0.07110.29835.0514.8490.642
25.4448-0.69543.35493.4333-0.49937.4610.1798-0.61590.0012-0.00080.0120.43920.4384-1.413-0.19180.1232-0.0883-0.03320.26980.02740.0704-7.7244.90615.491
322.9622-2.18690.134512.48693.27458.08470.50240.5203-0.0961-1.1319-0.26110.74290.5657-0.3843-0.24130.4695-0.0473-0.05680.12330.00090.0856-2.758-3.661.895
42.4356-0.36042.97192.3906-0.64577.2471-0.13420.20470.30130.1208-0.1265-0.2002-0.07150.51830.26070.08-0.0046-0.02860.04740.03860.085413.57111.4927.432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A386 - 391
2X-RAY DIFFRACTION2A392 - 525
3X-RAY DIFFRACTION3A526 - 543
4X-RAY DIFFRACTION4A544 - 684

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