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- PDB-4ats: Structure of the ORF273 protein from the Acidianus two-tailed virus -

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Basic information

Entry
Database: PDB / ID: 4ats
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 / OTHER / Resolution: 3.85 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
DepositionMay 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / 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
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STRUCTURAL PROTEIN ORF273


Theoretical massNumber of molelcules
Total (without water)34,3661
Polymers34,3661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.013, 101.013, 52.982
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: 34365.508 Da / Num. of mol.: 1
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 IQ PLYSS / References: UniProt: Q3V4T6
Has protein modificationY
Sequence detailsTHE PROTEIN INCLUDES AN N-TERMINAL HIS-TAG

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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: 1.97 Å3/Da / Density % sol: 37.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN AT 5.5 MG/ML IN 20 MM HEPES (PH 7.5) AND 100 MM NACL WAS MIXED TO 5%-15% PEG 8000, 0.2 M MGCL2, 0.1 M TRIS(PH 7-8). CRYSTALS WERE OBTAINED BY THE HANGING-DROP VAPOUR-DIFFUSION METHOD

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.181
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 3.85→101.01 Å / Num. obs: 2841 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 11.02 % / Biso Wilson estimate: 63.92 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 20.57
Reflection shellResolution: 3.85→3.93 Å / Redundancy: 11.63 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 5.51 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 3.85→46.92 Å / Cor.coef. Fo:Fc: 0.8648 / Cor.coef. Fo:Fc free: 0.8404 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.95
Details: RESIDUES 47-57 WERE NOT VISIBLE IN THE MAPS. REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 459 16.28 %RANDOM
Rwork0.2677 ---
obs0.2719 2819 99.02 %-
Displacement parametersBiso mean: 141.21 Å2
Baniso -1Baniso -2Baniso -3
1--14.5401 Å20 Å20 Å2
2---14.5401 Å20 Å2
3---29.0803 Å2
Refine analyzeLuzzati coordinate error obs: 1.379 Å
Refinement stepCycle: LAST / Resolution: 3.85→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 0 0 1951
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092000HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.062714HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d696SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it2000HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion19.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion257SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2181SEMIHARMONIC4
LS refinement shellResolution: 3.85→4.3 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3212 125 16.25 %
Rwork0.2893 644 -
all0.2947 769 -
obs--99.02 %
Refinement TLS params.Method: refined / Origin x: 27.2436 Å / Origin y: 8.3855 Å / Origin z: -11.0454 Å
111213212223313233
T0.4588 Å20.124 Å20.02 Å2-0.5186 Å2-0.1562 Å2--0.6079 Å2
L0 °2-0.3493 °2-0.3693 °2-0.1047 °21.3634 °2--1.4815 °2
S0.1244 Å °0.1518 Å °-0.1146 Å °0.3834 Å °0.0702 Å °-0.5853 Å °-0.3124 Å °-0.5903 Å °-0.1946 Å °

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