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- PDB-2j6b: crystal structure of AFV3-109, a highly conserved protein from cr... -

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Basic information

Entry
Database: PDB / ID: 2j6b
Titlecrystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses
ComponentsAFV3-109
KeywordsVIRAL PROTEIN / SULFOLOBUS / ACIDIANUS / VIRUS / CRENARCHAEA
Function / homologyUncharacterised protein PF08960, DUF1874 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesACIDIANUS FILAMENTOUS VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsKeller, J. / Leulliot, N. / Cambillau, C. / Campanacci, V. / Porciero, S. / Prangishvili, D. / Cortez, D. / Quevillon-Cheruel, S. / Van Tilbeurgh, H.
CitationJournal: Virol J. / Year: 2007
Title: Crystal Structure of Afv3-109, a Highly Conserved Protein from Crenarchaeal Viruses.
Authors: Keller, J. / Leulliot, N. / Cambillau, C. / Campanacci, V. / Porciero, S. / Prangishvili, D. / Forterre, P. / Cortez, D. / Quevillon-Cheruel, S. / Van Tilbeurgh, H.
History
DepositionSep 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AFV3-109


Theoretical massNumber of molelcules
Total (without water)12,3371
Polymers12,3371
Non-polymers00
Water5,495305
1
A: AFV3-109

A: AFV3-109


Theoretical massNumber of molelcules
Total (without water)24,6752
Polymers24,6752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)77.564, 77.564, 37.303
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2037-

HOH

21A-2103-

HOH

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Components

#1: Protein AFV3-109


Mass: 12337.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDIANUS FILAMENTOUS VIRUS 1 / Strain: 3 / Plasmid: PET9 / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.8 Å3/Da / Density % sol: 49.5 %
Crystal growpH: 4 / Details: 30% PEG4000, 0.2M NAAC, PH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 31813 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.1
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→67.12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.505 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1610 5.1 %RANDOM
Rwork0.16 ---
obs0.161 30242 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.3→67.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 0 305 1171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022888
X-RAY DIFFRACTIONr_bond_other_d0.0010.02601
X-RAY DIFFRACTIONr_angle_refined_deg1.421.991202
X-RAY DIFFRACTIONr_angle_other_deg0.81331492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54425.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66815176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.554153
X-RAY DIFFRACTIONr_chiral_restr0.070.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02154
X-RAY DIFFRACTIONr_nbd_refined0.2230.2173
X-RAY DIFFRACTIONr_nbd_other0.1920.2627
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2423
X-RAY DIFFRACTIONr_nbtor_other0.0860.2481
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.283
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3021.5728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4142895
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.613385
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.44.5307
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.233 121
Rwork0.219 2191

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