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- PDB-3vjj: Crystal Structure Analysis of the P9-1 -

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Basic information

Entry
Database: PDB / ID: 3vjj
TitleCrystal Structure Analysis of the P9-1
ComponentsP9-1
KeywordsVIRAL PROTEIN / Viroplasm
Function / homologyReovirus P9-like / Reovirus P9-like family / P9-1 protein
Function and homology information
Biological speciesRice black streaked dwarf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsAkita, F. / Higashiura, A. / Suzuki, M. / Tsukihara, T. / Nakagawa, A. / Omura, T.
CitationJournal: J.Virol. / Year: 2012
Title: Crystallographic analysis reveals octamerization of viroplasm matrix protein P9-1 of Rice black streaked dwarf virus
Authors: Akita, F. / Higashiura, A. / Shimizu, T. / Pu, Y. / Suzuki, M. / Uehara-Ichiki, T. / Sasaya, T. / Kanamaru, S. / Arisaka, F. / Tsukihara, T. / Nakagawa, A. / Omura, T.
History
DepositionOct 24, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P9-1
B: P9-1


Theoretical massNumber of molelcules
Total (without water)84,8882
Polymers84,8882
Non-polymers00
Water00
1
A: P9-1
B: P9-1

A: P9-1
B: P9-1

A: P9-1
B: P9-1

A: P9-1
B: P9-1


Theoretical massNumber of molelcules
Total (without water)339,5528
Polymers339,5528
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area25840 Å2
ΔGint-155 kcal/mol
Surface area107370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.284, 127.284, 143.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSchain A and (resseq 26:41 or resseq 63:126 or resseq...AA26 - 4126 - 41
12THRTHRLEULEUchain A and (resseq 26:41 or resseq 63:126 or resseq...AA63 - 12663 - 126
13GLUGLULEULEUchain A and (resseq 26:41 or resseq 63:126 or resseq...AA164 - 194164 - 194
14LEULEUVALVALchain A and (resseq 26:41 or resseq 63:126 or resseq...AA202 - 262202 - 262
15LYSLYSTHRTHRchain A and (resseq 26:41 or resseq 63:126 or resseq...AA265 - 313265 - 313
16THRTHRLYSLYSchain A and (resseq 26:41 or resseq 63:126 or resseq...AA324 - 346324 - 346
21GLUGLULYSLYSchain B and (resseq 26:41 or resseq 63:126 or resseq...BB26 - 4126 - 41
22THRTHRLEULEUchain B and (resseq 26:41 or resseq 63:126 or resseq...BB63 - 12663 - 126
23GLUGLULEULEUchain B and (resseq 26:41 or resseq 63:126 or resseq...BB164 - 194164 - 194
24LEULEUVALVALchain B and (resseq 26:41 or resseq 63:126 or resseq...BB202 - 262202 - 262
25LYSLYSTHRTHRchain B and (resseq 26:41 or resseq 63:126 or resseq...BB265 - 313265 - 313
26THRTHRLYSLYSchain B and (resseq 26:41 or resseq 63:126 or resseq...BB324 - 346324 - 346

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Components

#1: Protein P9-1 / Putative uncharacterized protein


Mass: 42444.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rice black streaked dwarf virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q913E4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.4264
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONPhoton Factory AR-NW12A20.97907, 0.97931, 0.96408
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 11, 2010
ADSC QUANTUM 2102CCDOct 11, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.979071
30.979311
40.964081
ReflectionResolution: 3→44.8 Å / Num. all: 24513 / Num. obs: 24512 / % possible obs: 100 % / Biso Wilson estimate: 92.8 Å2
Reflection shellHighest resolution: 3 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3→42.176 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.677 / SU ML: 0.35 / σ(F): 0 / Phase error: 36.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2928 974 4.25 %
Rwork0.2426 --
obs0.2449 22911 94.63 %
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 102.768 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 307.94 Å2 / Biso mean: 116.2418 Å2 / Biso min: 36.78 Å2
Baniso -1Baniso -2Baniso -3
1-14.088 Å20 Å2-0 Å2
2--14.088 Å20 Å2
3----28.1761 Å2
Refinement stepCycle: LAST / Resolution: 3→42.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4475 0 0 0 4475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134553
X-RAY DIFFRACTIONf_angle_d1.6546127
X-RAY DIFFRACTIONf_chiral_restr0.111695
X-RAY DIFFRACTIONf_plane_restr0.009775
X-RAY DIFFRACTIONf_dihedral_angle_d20.0341743
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2006X-RAY DIFFRACTIONPOSITIONAL0.073
12B2006X-RAY DIFFRACTIONPOSITIONAL0.073
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.15820.4011910.34722703279482
3.1582-3.3560.2853960.3053008310491
3.356-3.6150.30911420.26963122326496
3.615-3.97860.31641310.23623225335698
3.9786-4.55370.24291770.19193222339999
4.5537-5.73490.26291710.202133023473100
5.7349-42.18010.32471660.27263355352196
Refinement TLS params.Method: refined / Origin x: 15.8625 Å / Origin y: -33.7116 Å / Origin z: -34.001 Å
111213212223313233
T0.267 Å2-0.0393 Å20.0014 Å2-0.3451 Å2-0.0215 Å2--0.3222 Å2
L0.7361 °20.2993 °2-0.085 °2-0.8289 °2-0.199 °2--0.7641 °2
S0.0039 Å °0.3219 Å °0.0455 Å °-0.1497 Å °0.1909 Å °0.0282 Å °0.099 Å °-0.2109 Å °-0.0771 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 367
2X-RAY DIFFRACTION1allB26 - 367

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