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- PDB-2c0n: Crystal Structure of A197 from STIV -

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Basic information

Entry
Database: PDB / ID: 2c0n
TitleCrystal Structure of A197 from STIV
ComponentsA197
KeywordsVIRAL PROTEIN/TRANSFERASE / VIRAL PROTEIN-TRANSFERASE COMPLEX / VIRAL PROTEIN / VIRUS / ARCHAEA / CRENARCHAEA / ARCHAEAL VIRUS / CRENARCHAEAL VIRUS / THERMOPHILIC PROTEIN / THERMOPHILIC VIRUS / STIV / SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / SULFOLOBUS / GLYCOSYLTRANSFERASE / TRANSFERASE
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #40 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta / 1,4-DIETHYLENE DIOXIDE / NICKEL (II) ION / Uncharacterized protein
Function and homology information
Biological speciesSULFOLOBUS TURRETED ICOSAHEDRAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.86 Å
AuthorsLarson, E.T. / Reiter, D. / Young, M. / Lawrence, C.M.
Citation
Journal: J.Virol. / Year: 2006
Title: Structure of A197 from Sulfolobus Turreted Icosahedral Virus: A Crenarchaeal Viral Glycosyltransferase Exhibiting the Gt-A Fold.
Authors: Larson, E.T. / Reiter, D. / Young, M. / Lawrence, C.M.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2004
Title: The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life.
Authors: George Rice / Liang Tang / Kenneth Stedman / Francisco Roberto / Josh Spuhler / Eric Gillitzer / John E Johnson / Trevor Douglas / Mark Young /
Abstract: Of the three domains of life (Eukarya, Bacteria, and Archaea), the least understood is Archaea and its associated viruses. Many Archaea are extremophiles, with species that are capable of growth at ...Of the three domains of life (Eukarya, Bacteria, and Archaea), the least understood is Archaea and its associated viruses. Many Archaea are extremophiles, with species that are capable of growth at some of the highest temperatures and extremes of pH of all known organisms. Phylogenetic rRNA-encoding DNA analysis places many of the hyperthermophilic Archaea (species with an optimum growth > or = 80 degrees C) at the base of the universal tree of life, suggesting that thermophiles were among the first forms of life on earth. Very few viruses have been identified from Archaea as compared to Bacteria and Eukarya. We report here the structure of a hyperthermophilic virus isolated from an archaeal host found in hot springs in Yellowstone National Park. The sequence of the circular double-stranded DNA viral genome shows that it shares little similarity to other known genes in viruses or other organisms. By comparing the tertiary and quaternary structures of the coat protein of this virus with those of a bacterial and an animal virus, we find conformational relationships among all three, suggesting that some viruses may have a common ancestor that precedes the division into three domains of life >3 billion years ago.
History
DepositionSep 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_symmetry ..._pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A197
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6485
Polymers24,3171
Non-polymers3314
Water1,892105
1
A: A197
hetero molecules

A: A197
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,29710
Polymers48,6352
Non-polymers6628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)66.422, 70.560, 81.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1204-

NI

21A-2037-

HOH

DetailsTHE ANNOTATION FOR THIS ENTRY IS PREDICTED FROM THECRYSTAL STRUCTURE. HOWEVER, THE AUTHORS OF THIS ENTRYARE CURRENTLY INVESIGATING THE QUATERNARY STATE OFTHIS MOLECULE BY EXPERIMENTAL METHODS.

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Components

#1: Protein A197


Mass: 24317.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / Strain: ISOLATE YNPRC179
Description: STIV WAS ISOLATED FROM SULFOLOBUS SPECIES IN ACIDIC HOT SPRINGS (PH 2.9-3.9, 72-92 DEGREES C) IN THE RABBIT CREEK THERMAL AREA WITHIN MIDWAY GEYSER BASIN IN YELLOWSTONE NATIONAL PARK
Plasmid: PEXP14-STIVA197 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q6Q0L5
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL 6XHIS TAG WAS ADDED DURING CLONING, SELENOMETHIONINES IN PLACE OF METHIONINES

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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 Å3/Da / Density % sol: 37 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP VAPOR DIFFUSION IN 0.1 M MES(PH 6.5), 1.4 M (NH4)2SO4, 10% 1,4-DIOXANE; THEN CRYOPROTECTED BY A QUICK SOAK IN MOTHER LIQUOR PLUS 25% GLUCOSE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.978445, 0.879301
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2005 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9784451
20.8793011
ReflectionResolution: 1.86→30 Å / Num. obs: 15646 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.2
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.86→28.26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.369 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS MOTION DETERMINATION SERVER (PAINTER & MERRITT (2005) ACTA CRYST. D61, 465-471) WAS USED FOR SELECTION OF OPTIMAL TLS GROUPS USED IN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS MOTION DETERMINATION SERVER (PAINTER & MERRITT (2005) ACTA CRYST. D61, 465-471) WAS USED FOR SELECTION OF OPTIMAL TLS GROUPS USED IN FINAL REFINEMENT. AMINO ACIDS 139 TO 147 WERE NOT MODELED DUE TO THE ABSENCE OF INTERPRETABLE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 768 4.9 %RANDOM
Rwork0.171 ---
obs0.172 14813 95.5 %-
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: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.86→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 18 105 1718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221650
X-RAY DIFFRACTIONr_bond_other_d0.0050.021515
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9672219
X-RAY DIFFRACTIONr_angle_other_deg0.78633509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07522.85784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41415293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7321513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
X-RAY DIFFRACTIONr_nbd_refined0.2180.2303
X-RAY DIFFRACTIONr_nbd_other0.2090.21499
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2790
X-RAY DIFFRACTIONr_nbtor_other0.0850.2981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3020.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0580.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4231.51112
X-RAY DIFFRACTIONr_mcbond_other0.2591.5387
X-RAY DIFFRACTIONr_mcangle_it1.43721537
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7233783
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7034.5682
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: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 59 -
Rwork0.144 1119 -
obs--98.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6849-0.0892-0.45821.45260.32151.8367-0.0435-0.0699-0.25520.01030.0837-0.01260.23-0.0142-0.0402-0.01870.00920.0334-0.1097-0.0077-0.06538.272718.676438.8232
27.63992.0033-2.24237.42330.73425.3066-0.2266-0.0906-0.0842-0.02060.3759-0.32370.1720.3733-0.1493-0.02740.06060.0095-0.0784-0.0372-0.064247.276920.822939.7064
37.4593-4.17551.454211.54030.20424.8425-0.1066-0.5506-0.3624-0.080.2340.06690.15120.245-0.12740.00580.1294-0.020.0362-0.03890.003154.062315.725839.5354
45.992-1.72780.87332.7525-0.26571.8135-0.1050.0388-0.5190.0690.17450.06990.21880.1218-0.0694-0.0290.01780.0445-0.0774-0.0537-0.028345.300616.333233.3747
517.8557-7.2033-7.21488.41734.53963.39670.00110.035-0.164-0.1836-0.04920.01720.0879-0.18790.04810.09010.10480.0050.0624-0.1310.006258.45297.346820.3212
66.2335-5.57520.15435.3225-0.75831.9893-0.4314-0.07670.13150.44790.4115-0.2626-0.15990.41690.0199-0.02430.03610.00710.0202-0.1019-0.016152.719919.240228.4515
76.698-3.2746-0.77354.33080.78074.14890.14950.24070.2-0.1733-0.0914-0.1224-0.2502-0.0703-0.05810.0058-0.03390.0493-0.01310.0161-0.037241.813132.261322.2566
82.9807-0.72340.20641.42380.17924.28720.10170.2906-0.2233-0.0906-0.035-0.03240.42480.072-0.0667-0.0030.03570.02240.025-0.1021-0.011249.42414.402225.7273
97.42960.33392.46144.09582.18615.84670.11350.60140.124-0.27270.0536-0.2753-0.08530.5219-0.1671-0.03670.02380.07110.0561-0.0496-0.053854.857520.226122.0674
105.8486-3.7383-2.4876.61914.6654.5432-0.2048-0.43690.43630.3282-0.09230.23390.1156-0.24120.2971-0.0204-0.0239-0.0123-0.0266-0.0943-0.021727.537337.388837.1746
1110.475-0.819-3.11214.884-0.151111.0543-0.05210.60810.0144-0.14820.0032-0.05920.33750.04870.0489-0.049-0.0198-0.0199-0.06-0.0055-0.085332.639528.15323.4969
121.7931-0.98141.507418.6164-11.85118.6703-0.21440.2342-0.1462-0.11520.3022-0.11480.2682-0.2059-0.08770.0449-0.0530.0278-0.0766-0.0181-0.043523.79416.437637.3153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 27
2X-RAY DIFFRACTION2A28 - 41
3X-RAY DIFFRACTION3A42 - 52
4X-RAY DIFFRACTION4A53 - 67
5X-RAY DIFFRACTION5A68 - 81
6X-RAY DIFFRACTION6A82 - 91
7X-RAY DIFFRACTION7A92 - 107
8X-RAY DIFFRACTION8A108 - 150
9X-RAY DIFFRACTION9A151 - 166
10X-RAY DIFFRACTION10A167 - 176
11X-RAY DIFFRACTION11A177 - 189
12X-RAY DIFFRACTION12A190 - 198

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