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- PDB-3faj: Structure of the structural protein P131 of the archaeal virus Ac... -

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Basic information

Entry
Database: PDB / ID: 3faj
TitleStructure of the structural protein P131 of the archaeal virus Acidianus Two-tailed virus (ATV)
ComponentsPutative uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / archaeal virus / extremophiles / bicaudavirus / DNA-binding protein
Function / homologyUncharacterised protein DUF5062 / : / RIP/P131 family / Four Helix Bundle (Hemerythrin (Met), subunit A) / virion component / Up-down Bundle / Mainly Alpha / Structural protein ORF131
Function and homology information
Biological speciesAcidianus two-tailed virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsGoulet, A. / Vestergaard, G. / Scheele, U. / Campanacci, V. / Garrett, R.A. / Cambillau, C.
CitationJournal: To be Published
Title: Structure of the structural protein P131 of the archaeal virus Acidianus Two-tailed virus (ATV)
Authors: Goulet, A. / Vestergaard, G. / Scheele, U. / Campanacci, V. / Garrett, R.A. / Cambillau, C.
History
DepositionNov 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)16,5254
Polymers16,4191
Non-polymers1063
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.450, 62.450, 57.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Putative uncharacterized protein / ORF131


Mass: 16418.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus two-tailed virus / Gene: ORF131 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q3V4Q3
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 10% PEG 6000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Oct 30, 2008
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 13985 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rsym value: 0.063 / Net I/σ(I): 15.55
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.29 / Num. unique all: 2194 / Rsym value: 0.433 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→17.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.449 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19438 697 5 %RANDOM
Rwork0.17441 ---
obs0.17536 13273 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.161 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→17.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 3 116 894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022833
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.981128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6125113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.18524.10339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63915160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.351158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02636
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2437
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2582
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8271.5541
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0992841
X-RAY DIFFRACTIONr_scbond_it2.0333325
X-RAY DIFFRACTIONr_scangle_it3.3644.5280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 52 -
Rwork0.248 958 -
obs-959 99.02 %
Refinement TLS params.Method: refined / Origin x: -5.4515 Å / Origin y: 42.2761 Å / Origin z: 5.8693 Å
111213212223313233
T-0.1617 Å20.0031 Å2-0.0102 Å2--0.1982 Å2-0.0171 Å2---0.2145 Å2
L4.822 °20.1396 °2-0.8901 °2-2.5683 °20.1246 °2--2.3607 °2
S0.0687 Å °0.0314 Å °0.1296 Å °-0.0426 Å °-0.004 Å °0.0382 Å °-0.1162 Å °0.0781 Å °-0.0647 Å °

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