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- PDB-2wt0: Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre... -

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Entry
Database: PDB / ID: 2wt0
TitleGalectin domain of porcine adenovirus type 4 NADC-1 isolate fibre complexed with 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: 1.91 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 / 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.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)38,5416
Polymers37,9091
Non-polymers6315
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.450, 43.650, 63.900
Angle α, β, γ (deg.)90.00, 105.82, 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


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NO3 / NITRATE ION


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


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBETA-D-GALACTOSE (GAL): 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: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growpH: 8
Details: 35% (W/V) PEG 3350, 500 MM SODIUM NITRATE, 5 MM DITHIOTHREITOL, 40 MM N-ACETYL-LACTOSAMINE, 10 MM TRIS-HCL 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: Feb 17, 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: 1.91→35 Å / Num. obs: 22025 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 25.423 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.9
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5

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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: 1.91→35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.047 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23799 1126 5.1 %RANDOM
Rwork0.18163 ---
obs0.18443 20895 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.591 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20.31 Å2
2--2.13 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.91→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 42 163 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222467
X-RAY DIFFRACTIONr_bond_other_d0.0010.021650
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9893375
X-RAY DIFFRACTIONr_angle_other_deg0.85734036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30323.868106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06415376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.041514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_nbd_refined0.1930.2322
X-RAY DIFFRACTIONr_nbd_other0.1860.21541
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21116
X-RAY DIFFRACTIONr_nbtor_other0.0810.21289
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.53651524
X-RAY DIFFRACTIONr_mcbond_other0.9285594
X-RAY DIFFRACTIONr_mcangle_it3.44372483
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8437943
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3519892
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: 1.91→2.013 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 148 -
Rwork0.27 3071 -
obs--98.02 %
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)
119.60384.5526-0.36931.0577-0.08630.0099-0.04940.14910.0177-0.00190.04090.0086-0.0139-0.03060.00850.26830.0849-0.01790.33650.01140.2129-15.9173.32533.288
23.7012-0.5606-0.37661.3190.33243.6009-0.100900.1016-0.02250.0716-0.2187-0.02550.27240.02930.03070.0307-0.0080.1106-0.02270.043-12.1-1.82612.513
311.3528-9.05270.73877.2551-0.97454.191-0.9823-0.4472-0.12110.78780.4040.0303-0.0379-0.61350.57830.32860.03030.00210.64580.0580.3352-7.289-11.59525.811
43.5836-1.0642-0.03282.868-0.10592.6208-0.0848-0.05540.03670.04920.21330.21730.0206-0.2225-0.12840.03850.03160.01110.12050.03670.0293-35.4576.79617.753
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

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