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- PDB-2wt2: Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre... -

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Basic information

Entry
Database: PDB / ID: 2wt2
TitleGalectin domain of porcine adenovirus type 4 NADC-1 isolate fibre complexed with tri(N-acetyl-lactosamine)
ComponentsPUTATIVE FIBER PROTEIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


viral capsid / carbohydrate binding / cell adhesion / 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: 2.5 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 1.4Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE FIBER PROTEIN
B: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,41810
Polymers75,8182
Non-polymers2,6008
Water2,324129
1
A: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2095
Polymers37,9091
Non-polymers1,3004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2095
Polymers37,9091
Non-polymers1,3004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.130, 38.260, 86.520
Angle α, β, γ (deg.)90.00, 92.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2004-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99993, -0.00995, 0.00567), (0.00995, 0.99995, 0.00088), (-0.00568, -0.00082, 0.99998)
Vector: -1.4728, 15.02787, 43.1184)

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Components

#1: Protein PUTATIVE FIBER PROTEIN


Mass: 37909.156 Da / Num. of mol.: 2 / 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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2-1-2-1-2/a4-b1_b3-c1_c4-d1_d3-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(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.: 6 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBETA-D-GALACTOSE (GAL): PART OF POLYMER N-ACETYL-D-GLUCOSAMINE (NAG): PART OF POLYMER

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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: 1.9 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growpH: 8
Details: 10 MM TRIS-HCL, 1 MM EDTA, 28% (W/V) POLY-ETHYLENE GLYCOL 3350, 300 MM LITHIUM NITRATE, 5 MM DITHIOTHREITOL, 5 MM TRI(N-ACETYL-LACTOSAMINE), PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 3, 2009 / Details: BENT, VERTICALLY FOCUSSING MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 20441 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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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: 2.5→35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9 / SU B: 25.229 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1123 5.5 %THIN SHELLS
Rwork0.19989 ---
obs0.20365 19313 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.572 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.34 Å2
2---2.17 Å20 Å2
3---3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 176 129 5013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225022
X-RAY DIFFRACTIONr_bond_other_d0.0010.023352
X-RAY DIFFRACTIONr_angle_refined_deg1.2742.0126882
X-RAY DIFFRACTIONr_angle_other_deg0.78338178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91423.868212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32915750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4911528
X-RAY DIFFRACTIONr_chiral_restr0.0720.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02960
X-RAY DIFFRACTIONr_nbd_refined0.1810.02778
X-RAY DIFFRACTIONr_nbd_other0.1850.023301
X-RAY DIFFRACTIONr_nbtor_refined0.1720.022354
X-RAY DIFFRACTIONr_nbtor_other0.0810.022705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.02190
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.0226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.0268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.029
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.87553030
X-RAY DIFFRACTIONr_mcbond_other0.50851184
X-RAY DIFFRACTIONr_mcangle_it2.9574944
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.90671992
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.22691938
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: 2.5→2.634 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.355 129 -
Rwork0.324 2789 -
obs--100 %
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)
121.26274.3456-5.29044.75858.535627.0888-0.68280.1091-0.2141-0.81310.8124-0.2452-1.01121.2855-0.12960.5118-0.15830.05360.56260.02590.51623.749-5.459-47.454
24.1382-1.4521-0.61595.18050.51165.388-0.1161-0.6313-0.07560.58450.06920.11210.0166-0.13490.04690.0731-0.0180.01230.17410.02570.11213.773-15.747-30.904
34.55923.76284.40513.3937-1.28146.85290.281-0.67050.41090.4411-0.31611.42030.6264-1.13810.03510.7304-0.57270.27060.7274-0.25410.65622.505-24.008-40.359
45.3285-1.35690.20192.77570.20091.48560.05740.19280.0332-0.10160.0538-0.0914-0.0680.1462-0.11120.0353-0.01010.01650.0770.00120.045932.452-9.78-46.942
515.4978-11.771612.925619.3339-0.812419.0612-0.3243-0.8113-0.0227-0.50911.3814-0.7347-0.8329-0.2009-1.0570.2356-0.1128-0.01640.31170.08210.36662.2759.675-4.664
64.077-1.0694-0.85254.8550.5344.8787-0.0669-0.5896-0.10580.49110.1203-0.14510.021-0.0785-0.05340.0534-0.0092-0.01620.18090.03230.067712.312-0.58512.21
73.79990.73021.37712.3866-1.63019.7051-0.10910.425-0.56090.2573-0.7591.10420.0552-1.42870.86810.0805-0.1366-0.05230.5246-0.25590.57350.926-8.722.932
85.0517-1.4703-0.40074.54710.15061.50840.09470.2290.1184-0.111-0.0163-0.154-0.14010.1459-0.07840.0313-0.00880.03040.0632-0.00670.08330.7955.473-3.909
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 - 685
5X-RAY DIFFRACTION5B386 - 391
6X-RAY DIFFRACTION6B392 - 525
7X-RAY DIFFRACTION7B526 - 543
8X-RAY DIFFRACTION8B544 - 685

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