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- PDB-2wb6: Crystal structure of AFV1-102, a protein from the Acidianus Filam... -

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Basic information

Entry
Database: PDB / ID: 2wb6
TitleCrystal structure of AFV1-102, a protein from the Acidianus Filamentous Virus 1
ComponentsAFV1-102
KeywordsVIRAL PROTEIN / ARCHAEAL VIRUS
Function / homologyAspartate Aminotransferase, domain 1 - #90 / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / Uncharacterized protein ORF102
Function and homology information
Biological speciesACIDIANUS FILAMENTOUS VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsKeller, J. / Leulliot, N. / Collinet, B. / Campanacci, V. / Cambillau, C. / Pranghisvilli, D. / van Tilbeurgh, H.
CitationJournal: Protein Sci. / Year: 2009
Title: Crystal Structure of Afv1-102, a Protein from the Acidianus Filamentous Virus 1.
Authors: Keller, J. / Leulliot, N. / Collinet, B. / Campanacci, V. / Cambillau, C. / Pranghisvilli, D. / Van Tilbeurgh, H.
History
DepositionFeb 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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: AFV1-102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1213
Polymers15,0501
Non-polymers712
Water1,47782
1
A: AFV1-102
hetero molecules

A: AFV1-102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2416
Polymers30,0992
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area1230 Å2
ΔGint-10.4 kcal/mol
Surface area15410 Å2
MethodPQS
Unit cell
Length a, b, c (Å)62.890, 62.890, 110.837
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein AFV1-102


Mass: 15049.633 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDIANUS FILAMENTOUS VIRUS 1 / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q70LC3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 1.5-2M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 2% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→54.47 Å / Num. obs: 10006 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 34.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 38 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→54.47 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.236 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.611 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27431 481 4.8 %RANDOM
Rwork0.21339 ---
obs0.21619 9472 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→54.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 2 82 990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9871245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.55424.57135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61715191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.775153
X-RAY DIFFRACTIONr_chiral_restr0.0880.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02651
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2791.5570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4732918
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.813360
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.1314.5327
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr12.3053930
X-RAY DIFFRACTIONr_sphericity_free3.987385
X-RAY DIFFRACTIONr_sphericity_bonded5.4843914
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 38 -
Rwork0.241 675 -
obs--100 %

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