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- PDB-4x1z: Crystal structure of RHDVb P domain in complex with H type 2 -

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Basic information

Entry
Database: PDB / ID: 4x1z
TitleCrystal structure of RHDVb P domain in complex with H type 2
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: 1.36 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.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)69,84018
Polymers68,4602
Non-polymers1,38116
Water14,916828
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-137 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.170, 76.210, 107.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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 / Auth seq-ID: 238 - 569 / Label seq-ID: 1 - 332

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
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: 34229.785 Da / Num. of mol.: 2 / Fragment: UNP residues 238-569
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.: 2
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Fragment: ligand / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
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: Nov 5, 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: 1.3→20 Å / Num. obs: 151500 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 11.23 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.068 / Χ2: 1.022 / Net I/σ(I): 22.18 / Num. measured all: 2048689
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.3-1.330.7980.4541.89289311133397770.5486.3
1.33-1.370.9080.413.5629911093699140.44590.7
1.37-1.410.9740.3396.7313709210769107300.35399.6
1.41-1.450.9880.2689.2615859310379103780.277100
1.45-1.50.9910.21911.2915328410069100690.227100
1.5-1.550.9930.18412.89146567984698460.19100
1.55-1.610.9950.15714.57134287937693760.163100
1.61-1.680.9960.13417.82139780907790770.138100
1.68-1.750.9970.11620.54135624875287520.12100
1.75-1.840.9970.09924.06126694833983390.102100
1.84-1.940.9980.08528.38119587798579850.088100
1.94-2.060.9980.07532.56111160755075500.078100
2.06-2.20.9990.06837.1111302712871280.071100
2.2-2.370.9990.06439.2299435657765770.067100
2.37-2.60.9990.0641.8993188609960990.062100
2.6-2.910.9990.05444.0380814558755860.056100
2.91-3.360.9990.05248.5473043492849280.054100
3.36-4.110.9990.04751.5962358420542050.049100
4.11-5.810.9990.04251.6346771331433140.044100
5.810.9990.04151.5527188193618700.04396.6

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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: 1.36→19.997 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1324 6722 5 %
Rwork0.1078 127713 -
obs0.109 134435 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.51 Å2 / Biso mean: 15.8037 Å2 / Biso min: 6.51 Å2
Refinement stepCycle: final / Resolution: 1.36→19.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4836 0 86 831 5753
Biso mean--46.85 26.03 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075076
X-RAY DIFFRACTIONf_angle_d1.2466984
X-RAY DIFFRACTIONf_chiral_restr0.048800
X-RAY DIFFRACTIONf_plane_restr0.007916
X-RAY DIFFRACTIONf_dihedral_angle_d11.3071768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3610X-RAY DIFFRACTION3.607TORSIONAL
12B3610X-RAY DIFFRACTION3.607TORSIONAL
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 (%)
1.36-1.37550.15112080.11513962417096
1.3755-1.39160.13862210.10264198441999
1.3916-1.40860.16552240.091442434467100
1.4086-1.42640.14042200.090241884408100
1.4264-1.44520.11522230.079842264449100
1.4452-1.4650.11842250.079942754500100
1.465-1.48590.12472200.078241734393100
1.4859-1.50810.12822200.077442164436100
1.5081-1.53160.12712260.078742774503100
1.5316-1.55670.12612210.079942064427100
1.5567-1.58360.11962230.078142424465100
1.5836-1.61230.11622240.08142374461100
1.6123-1.64330.13142220.082142224444100
1.6433-1.67690.12352240.0842654489100
1.6769-1.71330.1222240.083242414465100
1.7133-1.75310.12932230.084342324455100
1.7531-1.7970.10452240.086142694493100
1.797-1.84550.13712230.090442194442100
1.8455-1.89980.11162240.09242814505100
1.8998-1.9610.11162250.094442704495100
1.961-2.03110.13272240.099342564480100
2.0311-2.11230.12612250.102142864511100
2.1123-2.20830.12172220.103942244446100
2.2083-2.32460.11272250.101542974522100
2.3246-2.470.13792260.110742804506100
2.47-2.66030.14092280.119243234551100
2.6603-2.92730.15022280.130643444572100
2.9273-3.34910.15372290.139243294558100
3.3491-4.21310.13972310.131743834614100
4.2131-19.99960.13412400.123145494789100

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