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- PDB-2wst: Head domain of porcine adenovirus type 4 NADC-1 isolate fibre -

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Basic information

Entry
Database: PDB / ID: 2wst
TitleHead domain of porcine adenovirus type 4 NADC-1 isolate fibre
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
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / 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 ...Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / 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. / Concanavalin A-like lectin/glucanase domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Galectin domain-containing protein
Similarity search - Component
Biological speciesPORCINE ADENOVIRUS 4
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 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 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Refinement description
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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 / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
E: PUTATIVE FIBER PROTEIN
F: PUTATIVE FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)133,7396
Polymers133,7396
Non-polymers00
Water724
1
A: PUTATIVE FIBER PROTEIN
B: PUTATIVE FIBER PROTEIN
C: PUTATIVE FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)66,8703
Polymers66,8703
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-25.2 kcal/mol
Surface area20920 Å2
MethodPISA
2
D: PUTATIVE FIBER PROTEIN
E: PUTATIVE FIBER PROTEIN
F: PUTATIVE FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)66,8703
Polymers66,8703
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-23.4 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.729, 145.439, 147.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 2 / Auth seq-ID: 116 - 291 / Label seq-ID: 33 - 208

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(-0.0436, 0.94089, 0.3359), (0.29495, 0.33335, -0.89548), (-0.95452, 0.06003, -0.29205)25.1174, 85.82668, 208.53441
2given(-0.03751, 0.29124, -0.95591), (0.94456, 0.3226, 0.06122), (0.3262, -0.90062, -0.28719)174.48288, -64.55092, 130.3685
3given(-0.33893, -0.0265, 0.94044), (0.94056, -0.03253, 0.33806), (0.02163, 0.99912, 0.03595)35.15798, -81.15913, -20.9661
4given(-0.89537, -0.27017, -0.35401), (-0.36731, 0.89751, 0.24404), (0.25179, 0.34854, -0.90284)220.09958, 9.47227, 74.58591
5given(0.29722, -0.95376, 0.04475), (0.04943, -0.03143, -0.99828), (0.95353, 0.29892, 0.0378)100.54362, 127.94822, -77.5533
6given(-0.04542, 0.94203, 0.33245), (0.28291, 0.3313, -0.90011), (-0.95807, 0.05317, -0.28156)25.44387, 87.61246, 208.58426
7given(0.30572, -0.95095, 0.04726), (0.04193, -0.03614, -0.99847), (0.9512, 0.30724, 0.02883)99.23951, 129.10413, -77.23893
8given(-0.33408, -0.03715, 0.94181), (0.94245, -0.02768, 0.33321), (0.01369, 0.99893, 0.04425)35.27816, -81.30988, -20.72046
9given(-0.89531, -0.27035, -0.35402), (-0.36706, 0.89804, 0.24248), (0.25237, 0.34704, -0.90326)220.06067, 9.52711, 74.68332
10given(-0.89399, -0.2711, -0.35678), (-0.3679, 0.89862, 0.23903), (0.25581, 0.34495, -0.90309)220.15413, 9.87801, 74.40134
11given(0.29329, -0.95456, 0.05292), (0.04189, -0.04247, -0.99822), (0.9551, 0.29499, 0.02753)100.40836, 129.55838, -76.60903
12given(-0.33171, -0.0242, 0.94307), (0.94326, -0.02459, 0.33114), (0.01518, 0.9994, 0.03098)33.9107, -81.38902, -19.7263
13given(-0.0223, -0.95304, -0.30203), (0.3302, -0.29217, 0.89755), (-0.94365, -0.07971, 0.32121)137.20383, -7.0309, 108.02687
14given(-0.03337, 0.32571, -0.94488), (-0.95474, -0.28997, -0.06623), (-0.29556, 0.89991, 0.32064)108.3404, 136.5936, 12.59673
15given(-0.02427, -0.95426, -0.29799), (0.31764, -0.28999, 0.90278), (-0.9479, -0.07274, 0.31015)137.15164, -6.55106, 108.63625

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Components

#1: Protein
PUTATIVE FIBER PROTEIN


Mass: 22289.850 Da / Num. of mol.: 6 / Fragment: HEAD DOMAIN, RESIDUES 116-291
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5.9 Å3/Da / Density % sol: 79.3 % / Description: NONE
Crystal growpH: 8
Details: 10 MM TRIS-HCL PH 8.0, 1 MM EDTA, 1-10% (W/V) POLY-ETHYLENE GLYCOL 8000, 1 M LITHIUM SULPHATE

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS KAPPACCD 2000 / Detector: CCD / Date: Jul 2, 2008 / Details: CONFOCAL MULTILAYER GRADED MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 45035 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.5
Reflection shellResolution: 3.2→3.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.9 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KNB

1knb


Resolution: 3.2→29.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 29.974 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20138 2026 4.8 %RANDOM
Rwork0.17302 ---
obs0.17442 40566 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20 Å2
2---0.11 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7980 0 0 4 7984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228160
X-RAY DIFFRACTIONr_bond_other_d0.0010.025184
X-RAY DIFFRACTIONr_angle_refined_deg1.271.96811178
X-RAY DIFFRACTIONr_angle_other_deg0.835312756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8151050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04824.909330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.017151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7161530
X-RAY DIFFRACTIONr_chiral_restr0.0670.21314
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219186
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021560
X-RAY DIFFRACTIONr_nbd_refined0.1990.21272
X-RAY DIFFRACTIONr_nbd_other0.1880.25077
X-RAY DIFFRACTIONr_nbtor_refined0.1810.24023
X-RAY DIFFRACTIONr_nbtor_other0.0880.24627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.23
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.51665238
X-RAY DIFFRACTIONr_mcbond_other0.64262148
X-RAY DIFFRACTIONr_mcangle_it2.49488502
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.10282922
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.17892676
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1026tight positional0.160.05
2B1026tight positional0.160.05
3C1026tight positional0.180.05
4D1026tight positional0.160.05
5E1026tight positional0.150.05
6F1026tight positional0.160.05
1A1168medium positional0.520.5
2B1168medium positional0.570.5
3C1168medium positional0.510.5
4D1168medium positional0.540.5
5E1168medium positional0.490.5
6F1168medium positional0.460.5
1A1026tight thermal0.40.5
2B1026tight thermal0.370.5
3C1026tight thermal0.40.5
4D1026tight thermal0.350.5
5E1026tight thermal0.360.5
6F1026tight thermal0.390.5
1A1168medium thermal0.362
2B1168medium thermal0.332
3C1168medium thermal0.352
4D1168medium thermal0.332
5E1168medium thermal0.322
6F1168medium thermal0.392
LS refinement shellResolution: 3.2→3.371 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 218 -
Rwork0.264 5769 -
obs--93.83 %
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)
15.8954-0.49172.28333.4509-0.75514.98720.20820.509-0.468-0.3232-0.00720.19430.45550.0782-0.2010.19980.0564-0.00530.0826-0.02470.0503112.54155.50770.984
23.2724-0.1320.34725.14221.55397.2996-0.0131-0.33210.48680.3062-0.15160.6159-0.4025-0.9910.16480.15310.0766-0.08060.1675-0.08890.313196.3173.96583.723
35.4761-1.3038-0.33955.01980.80763.9078-0.1181-0.5105-0.2040.53950.1171-0.18450.38410.10990.0010.11050.008-0.02190.1372-0.05320.0835118.53863.96596.683
44.53341.1911-0.07486.8144-1.43684.1948-0.07810.4117-0.2493-0.82950.21530.55960.5658-0.5596-0.13720.1477-0.1118-0.0960.35120.10820.144262.33646.87739.503
56.06471.95190.28044.7698-0.11216.07010.0893-0.1853-0.61450.0843-0.0138-0.59370.4390.4794-0.07550.2462-0.0255-0.04090.0660.0170.104179.27235.28758.156
64.6745-0.95011.0824.5314-1.25324.57-0.05460.29270.3509-0.2282-0.0446-0.3053-0.31210.23120.09920.1153-0.0187-0.03560.02520.01910.090184.23860.85748.963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A116 - 291
2X-RAY DIFFRACTION2B116 - 291
3X-RAY DIFFRACTION3C116 - 291
4X-RAY DIFFRACTION4D116 - 291
5X-RAY DIFFRACTION5E116 - 291
6X-RAY DIFFRACTION6F116 - 291

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