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- PDB-4art: STRUCTURE OF THE ORF273 PROTEIN FROM THE ACIDIANUS TWO-TAILED VIRUS -

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Basic information

Entry
Database: PDB / ID: 4art
TitleSTRUCTURE OF THE ORF273 PROTEIN FROM THE ACIDIANUS TWO-TAILED VIRUS
ComponentsSTRUCTURAL PROTEIN ORF273
KeywordsVIRAL PROTEIN / ARCHAEAL VIRUS / EXTREMOPHILES / BICAUDAVIRUS / HYPER-THERMOSTABILITY
Function / homology: / Acidianus two-tailed virus, ORF273 protein / virion component / Structural protein ORF273
Function and homology information
Biological speciesACIDIANUS TWO-TAILED VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsFelisberto-Rodrigues, C. / Ortiz-Lombardia, M.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of Atv(Orf273), a New Fold for a Thermo-and Acido-Stable Protein from the Acidianus Two-Tailed Virus.
Authors: Felisberto-Rodrigues, C. / Blangy, S. / Goulet, A. / Vestergaard, G. / Cambillau, C. / Garrett, R.A. / Ortiz-Lombardia, M.
History
DepositionApr 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: STRUCTURAL PROTEIN ORF273
B: STRUCTURAL PROTEIN ORF273
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5187
Polymers66,0462
Non-polymers4725
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-52.5 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.620, 78.620, 189.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein STRUCTURAL PROTEIN ORF273


Mass: 33023.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDIANUS TWO-TAILED VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): T7 EXPRESS IQ PLYSS / References: UniProt: Q3V4T6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.72 %
Description: SOLEIL DATASET (SE-SAD) WAS USED TO SOLVE THE STRUCTURE AND IN THE REFINEMENT OF THE FIRST MODEL. ESRF DATASET USED IMPROVE THE RESOLUTION TO 2.15 A, IN LATER REFINEMENT CYCLES.
Crystal growpH: 6
Details: PROTEIN SOLUTION AT 5 MG/ML IN 10 MM BICINE PH 8.5 AND 100 MM NACL WAS MIXED IN A 3:1 RATIO TO A SOLUTION CONTAINING 3.6% ISOPROPANOL AND 1.9 M AMMONIUM SULPHATE AS PRECIPITANT AGENTS IN 5 MM MGCL2 AND 2 MM AMP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID2910.91839
SYNCHROTRONSOLEIL PROXIMA 120.97911
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJul 25, 2010
ADSC QUANTUM 315r2CCDJun 3, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.918391
20.979111
ReflectionResolution: 2.15→50 Å / Num. obs: 32549 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.72 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.15→28.42 Å / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.239 / SU Rfree Blow DPI: 0.185
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY RESIDUES 44-54 AND 75- 82 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1660 5.1 %RANDOM
Rwork0.2024 ---
obs0.2041 32529 97.92 %-
Displacement parametersBiso mean: 50.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.4232 Å20 Å20 Å2
2---0.4232 Å20 Å2
3---0.8465 Å2
Refine analyzeLuzzati coordinate error obs: 0.354 Å
Refinement stepCycle: LAST / Resolution: 2.15→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 27 249 4193
LS refinement shellResolution: 2.15→2.22 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2547 166 5.53 %
Rwork0.2291 2838 -
all0.2307 3004 -
obs--97.92 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5073-0.47710.80152.6144-0.43553.4255-0.164-0.2318-0.18570.3480.14770.02880.4893-0.13290.01620.11910.09550.0673-0.01850.0235-0.246445.7033-12.59447.9308
20.7574-0.0626-0.12421.02950.3652.1584-0.0349-0.0093-0.0190.00510.0289-0.01990.06360.08780.0060.03610.03450.03150.06190.0304-0.179546.99112.210847.2129
35.22211.3471-1.16427.051-2.15193.6049-0.23290.72730.191-0.86990.62720.85870.8253-0.7733-0.39430.0892-0.2303-0.11590.12530.159-0.325121.25331.552264.2322
40.6522-0.1616-0.28581.1438-0.89593.4610.0216-0.06220.0324-0.02560.07890.13360.2259-0.2341-0.10050.0273-0.0057-0.00830.01190.01-0.210933.78878.115467.0611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 22:111
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 112:270
3X-RAY DIFFRACTION3CHAIN B AND RESSEQ 24:111
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 112:269

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