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- PDB-2zah: X-ray structure of Melon necrotic spot virus -

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Basic information

Entry
Database: PDB / ID: 2zah
TitleX-ray structure of Melon necrotic spot virus
ComponentsCoat protein
KeywordsVIRUS / plant virus / coat protein / b-annulus / tombusvirus / carmovirus / fungal vector / MNSV / Capsid protein / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / RNA binding
Similarity search - Function
Immunoglobulin-like - #4030 / Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Capsid protein / Capsid protein
Similarity search - Component
Biological speciesMelon necrotic spot virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsWada, Y. / Tsukihara, T. / Omura, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: X-ray structure of Melon necrotic spot virus
Authors: Wada, Y. / Tanaka, H. / Yamashita, E. / Kubo, C. / Ichiki-Uehara, T. / Nakazono-Nagaoka, E. / Omura, T. / Tsukihara, T.
History
DepositionOct 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Refinement description
Revision 1.3Nov 1, 2023Group: 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 / pdbx_struct_oper_list / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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_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: Coat protein
B: Coat protein
C: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5108
Polymers107,3493
Non-polymers1605
Water70339
1
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,450,588480
Polymers6,440,969180
Non-polymers9,619300
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 5


  • icosahedral pentamer
  • 538 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)537,54940
Polymers536,74715
Non-polymers80225
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 645 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)645,05948
Polymers644,09718
Non-polymers96230
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 538 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)537,54940
Polymers536,74715
Non-polymers80225
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)375.004, 375.004, 375.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12B
13C

NCS domain segments:

Dom-ID: 1 / Component-ID: 1 / Refine code: 1 / Auth seq-ID: 1 - 400 / Label seq-ID: 1 - 400

Ens-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS ensembles :
IDDetails
1A
2B
3C

NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)

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Components

#1: Protein Coat protein


Mass: 35783.160 Da / Num. of mol.: 3 / Fragment: Residues 60-390 / Source method: isolated from a natural source / Details: plant virus / Source: (natural) Melon necrotic spot virus / References: UniProt: Q3LHM1, UniProt: P19899*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS CONFIRMED THAT THIS POSITION IS TYR FROM THE ELECTRON DENSITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG2000, phosphate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.79→267 Å / Num. obs: 208594 / % possible obs: 97 % / Redundancy: 16.4 % / Rmerge(I) obs: 0.164
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0022refinement
MOSFLMdata reduction
SCALAdata scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TBV

2tbv


Resolution: 2.81→187.5 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.889 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22373 10487 5 %RANDOM
Rwork0.20839 ---
obs0.20916 198102 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.452 Å2
Refinement stepCycle: LAST / Resolution: 2.81→187.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7040 0 5 39 7084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02236005
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9449175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.354610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54123.4531535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.336155455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.93815250
X-RAY DIFFRACTIONr_chiral_restr0.0970.25760
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0227460
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.216692
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.224903
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.21251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.219
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.2385
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5021.523240
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88237255
X-RAY DIFFRACTIONr_scbond_it1.241314312
X-RAY DIFFRACTIONr_scangle_it2.1754.511920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2261tight positional0.020.05
1A2261tight thermal0.050.5
2B2272tight positional0.020.05
2B2272tight thermal0.050.5
3C2518tight positional0.020.05
3C2518tight thermal0.050.5
LS refinement shellResolution: 2.813→2.886 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 696 -
Rwork0.278 13012 -
obs--89.11 %

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