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- PDB-5w82: Crystal structure of Orsay virus delta protein N-terminal fragmen... -

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Basic information

Entry
Database: PDB / ID: 5w82
TitleCrystal structure of Orsay virus delta protein N-terminal fragment (aa 1-101)
ComponentsProtein delta
KeywordsVIRAL PROTEIN / pentameric alpha and beta barrel
Function / homologyProtein delta
Function and homology information
Biological speciesOrsay virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuo, Y.R. / Tao, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI122356 United States
CitationJournal: To be published
Title: To be published
Authors: Guo, Y.R. / Tao, Y.J.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Protein delta
B: Protein delta
D: Protein delta
E: Protein delta
A: Protein delta


Theoretical massNumber of molelcules
Total (without water)58,3265
Polymers58,3265
Non-polymers00
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34660 Å2
ΔGint-243 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.746, 58.220, 163.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein delta


Mass: 11665.256 Da / Num. of mol.: 5 / Fragment: N-terminal 1 to 101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orsay virus / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: E9KNV6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.32 Å3/Da / Density % sol: 47.08 % / Mosaicity: 0.426 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Ammonium sulfate, 0.1M Sodium acetate pH 4.6, 25% (w/w) PEG 4000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 49567 / % possible obs: 98.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.058 / Rrim(I) all: 0.122 / Χ2: 0.842 / Net I/σ(I): 4.5 / Num. measured all: 196759
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.833 / Num. unique all: 2333 / CC1/2: 0.998 / Rpim(I) all: 0.019 / Rrim(I) all: 0.042 / Χ2: 0.798 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.10_2152refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JIE

5jie


Resolution: 1.8→46.03 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.37
RfactorNum. reflection% reflection
Rfree0.226 2402 4.85 %
Rwork0.186 47111 -
obs0.188 49513 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.77 Å2 / Biso mean: 27.13 Å2 / Biso min: 10.7 Å2
Refinement stepCycle: final / Resolution: 1.8→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3987 0 0 552 4539
Biso mean---38.69 -
Num. residues----504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7979-1.83460.32911380.28242533267193
1.8346-1.87450.27631200.25612745286597
1.8745-1.91810.28271500.23032726287699
1.9181-1.96610.24681520.20962728288099
1.9661-2.01930.25751330.20122788292199
2.0193-2.07870.23111170.189328032920100
2.0787-2.14580.25621540.184727632917100
2.1458-2.22250.22131470.177627622909100
2.2225-2.31140.23031310.173728062937100
2.3114-2.41660.23641440.172528002944100
2.4166-2.5440.23881800.185327592939100
2.544-2.70340.21961410.182227782919100
2.7034-2.91210.22161470.1782825297299
2.9121-3.20510.19161350.16192804293999
3.2051-3.66870.19281110.16812847295898
3.6687-4.62150.18591540.15952797295197
4.6215-46.04830.25811480.21842847299594
Refinement TLS params.Method: refined / Origin x: 32.1196 Å / Origin y: 19.6859 Å / Origin z: 107.5558 Å
111213212223313233
T0.1365 Å2-0.0016 Å20.0025 Å2-0.1041 Å20.0003 Å2--0.1627 Å2
L0.1749 °20.0373 °20.0654 °2-0.1014 °2-0.0259 °2--1.6961 °2
S0.0029 Å °0.0348 Å °0.0057 Å °-0.0147 Å °0.0178 Å °-0.0016 Å °0.0044 Å °0.026 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLC1 - 101
2X-RAY DIFFRACTION1ALLC201 - 297
3X-RAY DIFFRACTION1ALLB1 - 101
4X-RAY DIFFRACTION1ALLB201 - 318
5X-RAY DIFFRACTION1ALLD1 - 101
6X-RAY DIFFRACTION1ALLD201 - 311
7X-RAY DIFFRACTION1ALLE1 - 101
8X-RAY DIFFRACTION1ALLE201 - 323
9X-RAY DIFFRACTION1ALLA1 - 100
10X-RAY DIFFRACTION1ALLA201 - 304

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