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- PDB-5e6t: Crystal structure of bovine norovirus P domain -

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Basic information

Entry
Database: PDB / ID: 5e6t
TitleCrystal structure of bovine norovirus P domain
ComponentsCapsid
KeywordsVIRAL PROTEIN / Protruding domain
Function / homology
Function and homology information


virion component => GO:0044423 / host cell cytoplasm / metal ion binding / cytoplasm
Similarity search - Function
Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus Bo/GIII/B309/2003/BEL
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsSingh, B.K. / Hansman, G.S.
Funding support Germany, China, 2items
OrganizationGrant numberCountry
CHS foundation Germany
Chinese Academy of Sciences China
CitationJournal: Virology / Year: 2015
Title: Structural analysis of bovine norovirus protruding domain.
Authors: Singh, B.K. / Koromyslova, A. / Hansman, G.S.
History
DepositionOct 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Capsid
B: Capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,23810
Polymers62,7142
Non-polymers5238
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-214 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.920, 63.860, 87.560
Angle α, β, γ (deg.)90.000, 115.060, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYchain AAA220 - 5071 - 288
2PHEPHEchain BBB224 - 5075 - 288

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Components

#1: Protein Capsid /


Mass: 31357.143 Da / Num. of mol.: 2 / Fragment: P DOMAIN, UNP residues 225-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Bo/GIII/B309/2003/BEL / Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E6Y5B1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, Zinc acetate, imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 3, 2014
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.2→40.81 Å / Num. obs: 28691 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 26.03 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.155 / Χ2: 0.897 / Net I/σ(I): 10.53 / Num. measured all: 144036
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.284.60.7790.6412.798756212819590.75692.1
2.26-2.320.8550.5583.6310731208220760.61899.7
2.32-2.380.8710.5443.910509201720090.60299.6
2.38-2.460.8890.4734.4210130196819590.52499.5
2.46-2.540.920.4354.79593188818810.48299.6
2.54-2.630.9390.3545.699055183818240.39399.2
2.63-2.730.9340.31568096178517720.35499.3
2.73-2.840.9610.2767.278610171717090.30699.5
2.84-2.960.9790.2238.918469163716330.24699.8
2.96-3.110.9850.18210.638146156115540.20199.6
3.11-3.280.9890.14712.577729150014910.16299.4
3.28-3.480.9910.12214.57021142414160.13599.4
3.48-3.720.9930.09417.286560133713330.10499.7
3.72-4.010.9950.08319.346608124912450.09199.7
4.01-4.40.9970.06423.035885114511380.07199.4
4.4-4.910.9960.06422.865229105210470.07199.5
4.91-5.680.9960.06322.0542689079010.07199.3
5.68-6.950.9950.06423.0541337957920.07199.6
6.95-9.830.9970.05724.3229236176060.06498.2
9.830.9960.05428.7315853563460.0697.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.04 Å40.81 Å
Translation7.04 Å40.81 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZL5
Resolution: 2.27→40.81 Å / FOM work R set: 0.8297 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 1311 5 %
Rwork0.1948 24901 -
obs0.1971 26212 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.07 Å2 / Biso mean: 26.05 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.27→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 8 218 4608
Biso mean--54.99 26.66 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054539
X-RAY DIFFRACTIONf_angle_d0.7836211
X-RAY DIFFRACTIONf_chiral_restr0.029684
X-RAY DIFFRACTIONf_plane_restr0.004832
X-RAY DIFFRACTIONf_dihedral_angle_d11.8691599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2540X-RAY DIFFRACTION8.21TORSIONAL
12B2540X-RAY DIFFRACTION8.21TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2701-2.3610.28811460.231427702916100
2.361-2.46840.3151440.231127342878100
2.4684-2.59850.26191440.22627472891100
2.5985-2.76130.30431440.22792742288699
2.7613-2.97440.25051460.210927562902100
2.9744-3.27360.26351440.200527532897100
3.2736-3.74710.22931460.188427712917100
3.7471-4.71980.20571470.157127862933100
4.7198-40.81670.20491500.182228422992100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.07140.5163-0.03521.4323-0.19021.5627-0.0243-0.04960.0222-0.1349-0.02250.12530.0249-0.10250.05340.09340.0268-0.01690.1341-0.01640.075990.3892-8.230194.0131
21.38130.41531.25021.09930.19812.1034-0.0553-0.05210.13290.135-0.04320.0844-0.3363-0.04430.08340.17920.0189-0.00690.13910.01010.113893.0749-1.2157112.3644
31.1979-0.00391.37854.39980.56913.1506-0.0527-0.56260.0190.3145-0.08820.6263-0.2872-0.6026-0.05130.26060.09650.02650.31960.01720.105791.0419-1.8899118.4737
42.0736-0.0651-0.18390.8693-0.20651.89880.0565-0.3861-0.03920.2285-0.08520.0354-0.09830.11540.00240.20980.0061-0.03830.17010.03330.1457102.8226-4.8639114.2682
50.71610.1566-0.01461.03510.63843.91670.1271-0.1327-0.07730.0771-0.1063-0.2586-0.73640.19950.0190.2207-0.0171-0.03590.16850.04740.1775105.52361.2332113.7582
62.22690.34970.02340.70670.12491.80610.0445-0.0666-0.19270.084-0.0511-0.08540.2772-0.00990.02110.19190.0081-0.00170.128-0.00140.119294.5766-12.3167100.4254
70.57870.0003-0.152.1819-0.35861.6976-0.35460.39470.3234-0.11140.46310.53140.0235-0.52110.05480.2357-0.0712-0.07360.45040.03130.221980.2618-8.153584.0922
81.63510.38080.62780.90390.05580.2416-0.00940.075-0.3476-0.01860.0187-0.06380.23190.0082-0.09260.1788-0.02560.00790.1922-0.04560.168189.2058-15.361185.4715
92.17760.83280.67811.4831-0.24281.3874-0.01080.3236-0.156-0.13250.28910.56690.4511-0.63860.11980.1549-0.0976-0.00480.49710.00430.335479.7893-16.069784.1661
102.59610.46630.25141.59150.12022.26730.3087-0.0982-0.1925-0.2144-0.05920.1057-0.18790.0104-0.2010.1960.07690.0210.16290.0020.202686.130710.5867100.9326
111.5867-0.6671-0.90431.3561-0.09691.20390.2589-0.07830.2610.0188-0.0714-0.1416-0.2237-0.0518-0.1170.21630.0132-0.00480.10910.01190.167697.658516.575493.7138
122.1430.3082-0.46851.6591-0.37962.36560.02890.10310.0767-0.05760.0065-0.1872-0.08510.1135-0.02560.1920.00840.00630.1210.02060.1364109.874313.201592.1644
133.1978-0.5393-1.32122.31370.72312.31730.0616-0.364-0.21650.1822-0.0956-0.30680.03160.29950.05210.2294-0.0025-0.05520.14630.04420.1595112.92368.978498.7241
141.8071-0.12821.02720.8958-0.47971.9016-0.0720.04290.48710.1378-0.08630.031-0.49920.13950.13930.36550.01990.09950.2017-0.02520.2782103.01925.678495.145
151.3094-0.2096-0.02290.73460.61961.05310.25-0.10390.373-0.030.0075-0.01-0.1070.0237-0.14290.2487-0.01010.09630.1571-0.00760.239693.528623.3949100.9818
162.08010.38090.49871.79460.64052.26680.2209-0.098-0.2518-0.12360.08-0.1762-0.1217-0.51780.04030.19610.03620.02540.21950.04460.135185.968812.118194.0126
171.9862-0.08390.15592.02720.17121.79790.29560.0577-0.0083-0.0724-0.22750.5051-0.1035-0.3129-0.04270.27410.0547-0.02650.22790.05540.426173.615115.904996.2427
180.49720.00010.27230.7934-0.15380.49970.12920.06590.48970.31790.07720.2695-0.51620.07810.15960.50360.10420.11830.12490.01420.314179.244923.8681102.3545
190.4093-0.2918-0.1862.15920.06711.41790.1750.30640.329-0.2901-0.19760.52480.0411-0.43060.37070.27520.21210.05380.25980.05240.270172.618723.07695.4901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 220 through 264 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 265 through 293 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 313 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 314 through 355 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 356 through 373 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 374 through 441 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 442 through 461 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 462 through 490 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 491 through 507 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 224 through 244 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 245 through 293 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 294 through 355 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 356 through 373 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 374 through 393 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 394 through 425 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 426 through 441 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 442 through 461 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 462 through 490 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 491 through 507 )B0

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