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- PDB-4x1x: Crystal structure of RHDVb P domain in complex with Lewis Y -

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Basic information

Entry
Database: PDB / ID: 4x1x
TitleCrystal structure of RHDVb P domain in complex with Lewis Y
ComponentsVP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Capsid spike / Protruding domain / HBGA binding
Function / homologyCalicivirus coat protein / Calicivirus coat protein / H type 2 antigen, alpha anomer / VP1
Function and homology information
Biological speciesRabbit hemorrhagic disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLeuthold, M.M. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Structural analysis of a rabbit hemorrhagic disease virus binding to histo-blood group antigens.
Authors: Leuthold, M.M. / Dalton, K.P. / Hansman, G.S.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / 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 / _chem_comp.name / _chem_comp.type / _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 2.1Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6829
Polymers68,8602
Non-polymers8227
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-24 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.440, 84.150, 62.660
Angle α, β, γ (deg.)90.000, 110.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA238 - 5693 - 334
2chain BBB236 - 5691 - 334
DetailsThe biological unit is a dimer. There is 1 biological unit in the asymmetric unit (chains A & B)

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Components

#1: Protein VP1


Mass: 34430.020 Da / Num. of mol.: 2 / Fragment: UNP residues 236-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabbit hemorrhagic disease virus / Gene: VP1 / Production host: Escherichia coli (E. coli) / References: UniProt: I7FLU3
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / H type 2 antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 2 antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Fragment: ligand / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: Lithium chloride, PEG 6000, Citric Acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984463 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984463 Å / Relative weight: 1
ReflectionResolution: 1.55→48.22 Å / Num. obs: 153487 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 14.29 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.085 / Χ2: 0.921 / Net I/σ(I): 7.46 / Num. measured all: 243456
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.590.5640.4841.341715312299107330.67187.3
1.59-1.630.6580.3911.651766011918110430.54292.7
1.63-1.680.7430.3281.921615211562104010.45490
1.68-1.730.8230.262.441696211294106280.36194.1
1.73-1.790.8670.2163.051687610938103560.394.7
1.79-1.850.9110.1793.65159951051699290.24994.4
1.85-1.920.9350.1444.53151721021395520.293.5
1.92-20.9520.1245.413737979389510.17291.4
2-2.090.970.0976.6813994939788780.13694.5
2.09-2.190.9750.0867.8513785902785800.1295
2.19-2.310.9820.0729.1212962853381140.10195.1
2.31-2.450.9860.06210.3311908805975470.08693.6
2.45-2.620.9880.05511.3110336759568650.07790.4
2.62-2.830.9920.04713.3210982711167660.06695.1
2.83-3.10.9930.0415.199782649160960.05693.9
3.1-3.470.9940.03617.228640590254860.05193
3.47-40.9960.0318.456941516446350.04289.8
4-4.90.9960.02721.216686439440920.03893.1
4.9-6.940.9970.02520.394928338730910.03591.3
6.940.9960.02622.182805185417440.03794.1

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x1w

4x1w


Resolution: 1.6→48.22 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 17.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 7012 4.99 %
Rwork0.1545 133427 -
obs0.1561 140439 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.88 Å2 / Biso mean: 18.7441 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 1.6→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 0 51 663 5560
Biso mean--23.74 26.66 -
Num. residues----666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055060
X-RAY DIFFRACTIONf_angle_d1.0816954
X-RAY DIFFRACTIONf_chiral_restr0.042788
X-RAY DIFFRACTIONf_plane_restr0.005919
X-RAY DIFFRACTIONf_dihedral_angle_d10.921750
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3576X-RAY DIFFRACTION6.021TORSIONAL
12B3576X-RAY DIFFRACTION6.021TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.29612210.24474422464393
1.6182-1.63720.31542350.24284446468193
1.6372-1.65720.27822320.24024389462192
1.6572-1.67820.28292240.23444157438189
1.6782-1.70030.25652310.22294414464592
1.7003-1.72350.22132350.20824474470995
1.7235-1.74820.22852400.1994613485395
1.7482-1.77430.22852380.20414438467694
1.7743-1.8020.25222370.19064520475795
1.802-1.83150.22052360.18474476471295
1.8315-1.86310.21212310.17414549478095
1.8631-1.8970.20592350.16864493472894
1.897-1.93350.16412310.15844401463293
1.9335-1.9730.17482330.15394452468593
1.973-2.01590.19582260.16374262448889
2.0159-2.06270.19222410.1584554479595
2.0627-2.11430.19662370.15564496473395
2.1143-2.17150.19732380.15264520475895
2.1715-2.23540.16472470.14034575482295
2.2354-2.30750.1592350.13774489472495
2.3075-2.390.17392430.13834526476994
2.39-2.48570.17432260.14264405463193
2.4857-2.59880.17022280.1434304453289
2.5988-2.73580.15842430.1444484472795
2.7358-2.90720.17622350.14434534476995
2.9072-3.13170.18332330.1424476470994
3.1317-3.44670.18282300.14544427465793
3.4467-3.94530.15812280.14364281450990
3.9453-4.96980.15522330.12234445467893
4.9698-48.24270.15712300.14094405463592
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)
11.2623-1.6137-0.32465.82764.45945.0611-0.1192-0.075-0.0360.42840.1439-0.03570.1889-0.0502-0.03360.11570.00810.00030.09340.02540.11-36.483327.1939-33.1228
21.0619-0.2027-0.22662.17410.5220.4728-0.050.0453-0.1575-0.01580.06020.39810.0612-0.1034-0.00950.08160.0035-0.01040.120.00460.1689-43.026118.1286-38.5683
34.26-1.4108-3.12331.89871.52883.9975-0.1583-0.0531-0.26570.0244-0.03980.3720.226-0.06860.21460.1223-0.0122-0.04090.09320.00490.2179-36.0463-0.8195-47.4016
42.54121.48171.38335.455-1.65112.95190.06190.4152-0.3356-0.4648-0.0148-0.06610.1580.274-0.05040.09570.0306-0.05170.1582-0.0550.1782-34.454211.8916-53.8896
50.7067-0.59990.04340.95210.00210.60250.0360.0265-0.1372-0.1265-0.05470.25170.0873-0.11120.00550.1071-0.0159-0.03110.1005-0.01750.1449-32.14745.2088-49.8187
60.8727-0.3057-0.54091.00680.27451.00690.03140.0436-0.0212-0.1484-0.0630.2331-0.0981-0.11170.01660.11050.0093-0.04060.10050.00250.1619-39.829523.9952-46.8212
71.9146-1.059-0.00991.17160.43441.32610.0986-0.12310.11450.0660.11020.3282-0.187-0.3136-0.17160.09380.00880.00330.1227-0.00160.2094-41.295425.413-35.558
81.5205-0.29741.02151.70020.6712.6288-0.0103-0.01470.1091-0.03790.02610.2914-0.2697-0.079-0.02360.12690.03130.00230.11070.0070.1811-44.871237.6912-36.4818
91.57670.1276-0.80490.5862-0.13362.0578-0.00120.04350.02090.0577-0.01580.0236-0.0761-0.12160.02550.08830.00410.0040.0794-0.00390.0808-23.341818.8495-22.5556
104.92080.1322-0.0153.20661.75485.6184-0.01830.15970.0278-0.39210.0444-0.23130.07040.14760.00850.13220.0080.03440.12490.03060.0685-6.8376.8453-49.7145
110.43410.024-0.18920.73920.0151.35130.00130.0340.0157-0.01380.0133-0.02730.00840.0492-0.01350.08480.00160.01570.10120.00530.1069-11.355610.6203-38.7043
120.8607-0.0520.59971.33751.95013.4961-0.0136-0.1145-0.02880.1391-0.04640.06040.2337-0.09470.070.10420.00310.02540.08360.03070.0908-18.40598.9965-20.8882
131.0308-0.4066-0.44020.62640.22891.5207-0.1131-0.0585-0.11750.0607-0.01990.10290.1187-0.10730.10260.1079-0.01370.01770.1053-0.00350.0968-26.840315.8044-13.5147
144.57091.61170.79573.1787-1.72644.4436-0.0086-0.34530.04990.2698-0.1559-0.0235-0.0343-0.09970.18820.16190.02980.04440.1553-0.03890.0823-29.255917.4053-3.2979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 238 through 260 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 261 through 297 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 334 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 354 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 436 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 437 through 476 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 477 through 510 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 511 through 569 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 236 through 297 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 298 through 314 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 315 through 436 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 437 through 476 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 477 through 551 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 552 through 569 )B0

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