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- PDB-5eft: Structural Basis for Specific Recognition of ssDNA by SRBSDV P9-1... -

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Basic information

Entry
Database: PDB / ID: 5eft
TitleStructural Basis for Specific Recognition of ssDNA by SRBSDV P9-1 Octamers
Components(p9-1) x 2
KeywordsVIRAL PROTEIN / Specific Recognition / ssDNA / SRBSDV P9-1 / Octamers
Function / homologyReovirus P9-like / Reovirus P9-like family / p9-1
Function and homology information
Biological speciesRice black-streaked dwarf virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLi, X.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31460460 China
National Natural Science Foundation of China21132003 China
CitationJournal: To Be Published
Title: Structural Basis for Specific Recognition of ssDNA by SRBSDV P9-1 Octamers
Authors: Li, X.Y.
History
DepositionOct 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_prerelease_seq / pdbx_struct_oper_list / 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_oper_list.symmetry_operation / _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: p9-1
B: p9-1
C: p9-1
D: p9-1
E: p9-1
F: p9-1
G: p9-1
H: p9-1


Theoretical massNumber of molelcules
Total (without water)155,2038
Polymers155,2038
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-60 kcal/mol
Surface area51920 Å2
Unit cell
Length a, b, c (Å)118.520, 155.720, 157.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVALAA332 - 3471 - 16
21ALAALAVALVALCC332 - 3471 - 16
12ALAALAVALVALAA332 - 3471 - 16
22ALAALAVALVALEE332 - 3471 - 16
13ALAALAVALVALAA332 - 3471 - 16
23ALAALAVALVALGG332 - 3471 - 16
14LEULEUPHEPHEBB4 - 3241 - 321
24LEULEUPHEPHEDD4 - 3241 - 321
15LEULEUPHEPHEBB4 - 3241 - 321
25LEULEUPHEPHEFF4 - 3241 - 321
16LEULEUPHEPHEBB4 - 3241 - 321
26LEULEUPHEPHEHH4 - 3241 - 321
17ALAALAVALVALCC332 - 3471 - 16
27ALAALAVALVALEE332 - 3471 - 16
18ALAALAVALVALCC332 - 3471 - 16
28ALAALAVALVALGG332 - 3471 - 16
19LEULEUPHEPHEDD4 - 3241 - 321
29LEULEUPHEPHEFF4 - 3241 - 321
110LEULEUPHEPHEDD4 - 3241 - 321
210LEULEUPHEPHEHH4 - 3241 - 321
111ALAALAVALVALEE332 - 3471 - 16
211ALAALAVALVALGG332 - 3471 - 16
112LEULEUPHEPHEFF4 - 3241 - 321
212LEULEUPHEPHEHH4 - 3241 - 321

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein/peptide
p9-1


Mass: 1725.936 Da / Num. of mol.: 4 / Fragment: C-terminal peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rice black-streaked dwarf virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: B6SCH3
#2: Protein
p9-1


Mass: 37074.844 Da / Num. of mol.: 4 / Fragment: UNP residues 4-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rice black-streaked dwarf virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: B6SCH3

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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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Trimethylamine N-oxide dihydrate, 100 mM Tris-HCl, 16% Polyethylene glycol monomethyl ether 3000

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Data collection

DiffractionMean temperature: 195 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: RIGAKU AFC9 / Detector: DIFFRACTOMETER / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.18→29.6 Å / Num. obs: 65431 / % possible obs: 99.3 % / Redundancy: 5.4 % / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
Cootdata reduction
Cootphasing
RefinementResolution: 2.5→29.6 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.917 / SU B: 14.068 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.537 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2842 2566 5.1 %RANDOM
Rwork0.2534 ---
obs0.255 47882 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 249.72 Å2 / Biso mean: 88.171 Å2 / Biso min: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å2-0 Å2
2---2.79 Å2-0 Å2
3---5.47 Å2
Refinement stepCycle: final / Resolution: 2.5→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8792 0 0 0 8792
Num. residues----1084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198944
X-RAY DIFFRACTIONr_bond_other_d0.0040.028732
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.98412068
X-RAY DIFFRACTIONr_angle_other_deg0.858320036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37851056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.923.905420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.198151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7161556
X-RAY DIFFRACTIONr_chiral_restr0.070.21396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029836
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022068
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6770.02
12C6770.02
21A6800.02
22E6800.02
31A6780.02
32G6780.02
41B165540.01
42D165540.01
51B165670.01
52F165670.01
61B165670.01
62H165670.01
71C6780.01
72E6780.01
81C6770.01
82G6770.01
91D165630.01
92F165630.01
101D165620.01
102H165620.01
111E6810.01
112G6810.01
121F165750.01
122H165750.01
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 194 -
Rwork0.408 3490 -
all-3684 -
obs--99.59 %
Refinement TLS params.L11 esd: 0 °2 / L12 esd: 0 °2 / L13 esd: 0 °2 / L22 esd: 0 °2 / L23 esd: 0 °2 / L33 esd: 0 °2 / S11 esd: 0 Å ° / S12 esd: 0 Å ° / S13 esd: 0 Å ° / S21 esd: 0 Å ° / S22 esd: 0 Å ° / S23 esd: 0 Å ° / S31 esd: 0 Å ° / S32 esd: 0 Å ° / S33 esd: 0 Å ° / T11 esd: 0 Å2 / T12 esd: 0 Å2 / T13 esd: 0 Å2 / T22 esd: 0 Å2 / T23 esd: 0 Å2 / T33 esd: 0 Å2

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