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- PDB-3fbl: Crystal structure of ORF132 of the archaeal virus Acidianus Filam... -

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Basic information

Entry
Database: PDB / ID: 3fbl
TitleCrystal structure of ORF132 of the archaeal virus Acidianus Filamentous Virus 1 (AFV1)
ComponentsPutative uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / AFV1 / archaeal virus / extremophiles / lipothrixviridae / DNA-binding protein
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #800 / helical viral capsid / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / DNA binding / Mainly Alpha / Major capsid protein 2
Function and homology information
Biological speciesAcidianus filamentous virus 1
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.95 Å
AuthorsGoulet, A. / Leulliot, N. / Prangishvili, D. / van Tilbeurgh, H. / Campanacci, V. / Cambillau, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage
Authors: Goulet, A. / Blangy, S. / Redder, P. / Prangishvili, D. / Felisberto-Rodrigues, C. / Forterre, P. / Campanacci, V. / Cambillau, C.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2042
Polymers9,1691
Non-polymers351
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.353, 47.576, 60.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein


Mass: 9168.595 Da / Num. of mol.: 1 / Fragment: ORF132 domain, residues 51-132
Source method: isolated from a genetically manipulated source
Details: The protein expressed is a fusion with thioredoxin in N-terminal position. An hexahistidine-tag and a TEV protease cleavage site are inserted between thioredoxin and the protein of interest
Source: (gene. exp.) Acidianus filamentous virus 1 / Gene: AFV1_ORF132 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q70LC7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN USED FOR CRYSTALLIZATION IS THE FULL-LENGTH FORM, BUT THE PROTEIN IS DEGRADED IN ...THE PROTEIN USED FOR CRYSTALLIZATION IS THE FULL-LENGTH FORM, BUT THE PROTEIN IS DEGRADED IN CRYSTALLIZATION PLATES AND THUS FRAGMENT FROM RESIDUE 51 TO THE C-TERMINAL CRYSTALLIZES. THE N-TERMINUS 50 RESIDUES INCLUDING THE EXPRESSION TAG GLY 1 ARE SHOWN BELOW; GVNKKYRQDSKDRYQYKQYIYRSIGGIVPPEMAETVTANQTAQWEAGFTP

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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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 8000, 0.025 mM Na2HPO4/KH2PO4, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→25.6 Å / Num. obs: 6349 / % possible obs: 100 % / Redundancy: 76 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 136.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 76 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 89 / Num. unique all: 902 / Rsym value: 0.066 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→18 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.807 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19619 795 12.6 %RANDOM
Rwork0.15699 ---
obs0.16203 5512 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms657 0 1 106 764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022670
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.962901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.726585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36224.07427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07715131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.138153
X-RAY DIFFRACTIONr_chiral_restr0.0770.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02488
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2318
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2481
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.021.5431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2452661
X-RAY DIFFRACTIONr_scbond_it2.3543285
X-RAY DIFFRACTIONr_scangle_it3.7114.5238
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 60 -
Rwork0.157 403 -
obs-388 100 %

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