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

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Basic information

Entry
Database: PDB / ID: 2wsu
TitleGalectin domain of porcine adenovirus type 4 NADC-1 isolate fibre
ComponentsPUTATIVE FIBER PROTEIN
KeywordsVIRAL PROTEIN / CARBOHYDRATE RECOGNITION DOMAIN / TANDEM-REPEAT-TYPE
Function / homology
Function and homology information


galactoside binding / viral capsid / carbohydrate binding / cell adhesion / membrane raft / virion attachment to host cell / plasma membrane
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 1.4Dec 20, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: PUTATIVE FIBER PROTEIN
D: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,93322
Polymers151,6374
Non-polymers1,29718
Water11,259625
1
A: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1875
Polymers37,9091
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2796
Polymers37,9091
Non-polymers3705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2796
Polymers37,9091
Non-polymers3705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PUTATIVE FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1875
Polymers37,9091
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.691, 77.325, 94.111
Angle α, β, γ (deg.)90.00, 101.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99705, 0.07336, -0.02248), (0.07521, 0.99245, -0.0969), (0.0152, -0.0983, -0.99504)45.9929, 7.05912, 186.37505
2given(0.99957, -0.0128, 0.02642), (0.01307, 0.99987, -0.00992), (-0.02629, 0.01026, 0.9996)7.3938, -19.15178, -45.50405
3given(-0.99817, 0.06025, -0.00542), (0.06049, 0.99529, -0.07572), (0.00083, -0.07591, -0.99711)54.16811, -14.0609, 140.37973
4given(-0.99818, 0.05943, -0.01005), (0.06007, 0.99455, -0.08525), (0.00493, -0.0857, -0.99631)54.74946, -12.79937, 140.47636
5given(0.99977, -0.01485, -0.01562), (0.0145, 0.99965, -0.02196), (0.01594, 0.02173, 0.99964)11.21296, -17.72412, -46.82848
6given(-0.99865, 0.04733, 0.02148), (0.04579, 0.9967, -0.06708), (-0.02458, -0.066, -0.99752)63.42914, 1.63454, 93.90726

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Components

#1: Protein
PUTATIVE FIBER PROTEIN


Mass: 37909.156 Da / Num. of mol.: 4 / 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O

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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: 37.6 % / Description: NONE
Crystal growpH: 8
Details: 10 MM TRIS-HCL PH 8.0, 1 MM EDTA, 25% (W/V) POLY-ETHYLENE GLYCOL 3350, 500 MM SODIUM NITRATE, 2 MM SIALIC ACID

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 20, 2008 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 89027 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.7 / % possible all: 90.1

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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 1A3K

1a3k


Resolution: 1.9→35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.559 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25915 2124 2.4 %THIN SHELLS
Rwork0.20642 ---
obs0.20772 86627 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-1.08 Å2
2---0.62 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9501 0 84 625 10210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229901
X-RAY DIFFRACTIONr_bond_other_d0.0010.026646
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.97813537
X-RAY DIFFRACTIONr_angle_other_deg0.822316272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10951219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38523.875431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.171151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3051556
X-RAY DIFFRACTIONr_chiral_restr0.0780.21544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021948
X-RAY DIFFRACTIONr_nbd_refined0.1910.021416
X-RAY DIFFRACTIONr_nbd_other0.1870.026407
X-RAY DIFFRACTIONr_nbtor_refined0.170.024568
X-RAY DIFFRACTIONr_nbtor_other0.0820.025269
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.02531
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.0231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.02106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.0230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.16176152
X-RAY DIFFRACTIONr_mcbond_other1.24372401
X-RAY DIFFRACTIONr_mcangle_it4.329910050
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.22293749
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.961113487
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: 1.901→2.003 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.327 293 -
Rwork0.298 11703 -
obs--89.31 %
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)
112.4618-0.9805-8.80821.756-2.762613.3483-0.3915-0.8805-1.005-0.04520.04560.24260.47650.64410.34590.3252-0.0214-0.02930.28030.07420.305322.67527.497.098
26.34120.14482.09674.22550.51866.0456-0.24420.99060.3353-0.5484-0.0197-0.3051-0.12720.59740.26390.1039-0.03620.00180.18230.08350.090540.16136.5587.654
310.08590.42331.588210.4105-2.3496.3531-0.13710.12820.4541-0.5618-0.50830.6578-0.3677-0.37650.64540.2040.1013-0.1190.31680.01740.50925.49245.18389.381
45.92661.26953.11144.12451.30373.3540.1383-0.58580.07520.5154-0.0997-0.2260.3332-0.3673-0.03860.1393-0.0335-0.03450.07460.00580.034946.82131.006111.4
521.682-10.05380.95454.7206-0.40430.0720.13360.111-0.2365-0.0876-0.0071-0.06150.0175-0.0003-0.12650.4203-0.02530.00980.371-0.09140.515423.26427.32587.426
63.836-1.03990.0943.5289-0.37263.6264-0.1865-0.59030.11750.60350.13220.1742-0.1355-0.18830.05430.15940.0407-0.0160.1515-0.0630.08876.58837.99196.01
77.6382-1.73820.576816.4655-6.254113.661-0.2579-0.0405-0.08130.3809-0.4282-0.60060.12150.10580.68620.1214-0.0339-0.03420.2926-0.06210.48121.70245.26793.399
86.9634-0.65833.84523.1055-0.47033.64330.01620.37230.1289-0.1801-0.10580.05910.12480.22490.08960.03880.0144-0.00110.02740.00150.0128-0.89430.48473.12
920.2141-0.1161.229821.7235-11.49377.1446-0.40910.7233-0.0257-1.34930.5825-0.17380.4076-0.0129-0.17340.37360.04380.04210.3381-0.07690.25481.77928.83754.386
1015.434-1.94-8.7461.3496-1.38210.561-0.3207-1.0319-0.9315-0.1470.13270.29780.68550.60390.18810.30330.02820.05110.29310.05670.281831.9678.1451.187
113.6810.5079-0.72743.47680.49434.4129-0.07750.53970.0439-0.51850.0246-0.2489-0.110.10160.05290.129-0.0099-0.00780.160.05770.106749.42517.05241.429
124.5949-0.74370.222419.0152-6.01452.05310.11430.06531.0759-1.1389-0.15921.3410.2391-0.27370.04490.18960.1989-0.47981.0173-0.79021.790834.70325.83843.729
138.33181.39125.25813.93751.35225.24930.1796-0.30590.21160.4101-0.1947-0.14290.4163-0.17240.01510.1082-0.022-0.01850.0188-0.00450.02156.73411.44965.052
147.3239-6.3523-2.666719.6595.503110.5377-0.2642-0.4070.1810.61350.5821-0.5925-0.1215-0.2209-0.31790.1761-0.01860.04510.23120.00280.195454.4410.18483.888
1519.6915-3.16061.5881.0458-2.726611.86550.18770.2419-1.0108-0.28750.04060.13560.9723-0.0301-0.22840.4282-0.08880.08150.4537-0.14020.419132.7847.78741.254
166.095-1.58132.32554.5553-1.01155.1926-0.3874-0.81330.26950.63880.20850.2184-0.1964-0.39930.17890.1020.05920.00680.1192-0.04980.076515.83218.19650.134
177.3974-0.39680.678313.4772-3.227113.3965-0.1679-0.11630.18580.5643-0.4795-0.3881-0.48180.70150.64740.1112-0.0448-0.05630.2608-0.01690.4630.58625.99748.223
187.0505-2.16864.72343.0691-1.76115.0290.5580.8945-0.2433-0.3292-0.31070.07870.66180.7893-0.24730.12680.114-0.02780.1411-0.04550.03518.57211.22527.098
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
9X-RAY DIFFRACTION9B686 - 691
10X-RAY DIFFRACTION10C386 - 391
11X-RAY DIFFRACTION11C392 - 525
12X-RAY DIFFRACTION12C526 - 543
13X-RAY DIFFRACTION13C544 - 685
14X-RAY DIFFRACTION14C686 - 691
15X-RAY DIFFRACTION15D386 - 391
16X-RAY DIFFRACTION16D392 - 525
17X-RAY DIFFRACTION17D526 - 543
18X-RAY DIFFRACTION18D544 - 684

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