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- PDB-6bo3: Structure Determination of A223, a turret protein in Sulfolobus t... -

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Basic information

Entry
Database: PDB / ID: 6bo3
TitleStructure Determination of A223, a turret protein in Sulfolobus turreted icosahedral virus, using an iterative hybrid approach
ComponentsUncharacterized protein
KeywordsVIRAL PROTEIN / A223 / STIV / C381 / twin / twinning / 3j31 / 4IL7
Function / homologyJelly Rolls - #1300 / : / A223 penton protein second domain / Jelly Rolls / Sandwich / Mainly Beta / A223 penton protein C-terminal domain-containing protein
Function and homology information
Biological speciesSulfolobus turreted icosahedral virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsSendamarai, A.K. / Veesler, D. / Fu, C.Y. / Marceau, C. / Larson, E.T. / Johnson, J.E. / Lawrence, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: STRUCTURAL CHARACTERIZATION OF A223, A STRUCTURAL PROTEIN FROM SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS (STIV)
Authors: Sendamarai, A.K. / Lawrence, C.M.
History
DepositionNov 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)50,5732
Polymers50,5732
Non-polymers00
Water91951
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,2871
Polymers25,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,2871
Polymers25,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.995, 56.995, 272.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVAL2AA20 - 13120 - 131
21VALVAL2BB20 - 13120 - 131
12TYRTYR6AA140 - 177140 - 177
22TYRTYR6BB140 - 177140 - 177
13SERSER6AA183 - 223183 - 223
23SERSER6BB183 - 223183 - 223

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.987803, -0.15546, 0.008799), (-0.155699, 0.985543, -0.06681), (0.001714, -0.067365, -0.997727)3.62941, 2.065, 47.83965

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Components

#1: Protein Uncharacterized protein


Mass: 25286.529 Da / Num. of mol.: 2 / Mutation: L208M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus turreted icosahedral virus 1
Gene: A223 / Plasmid: pDEST14 / Details (production host): Invitrogen / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): CodonPlus (DE3) RIL / References: UniProt: Q6Q0L4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.62 Å3/Da / Density meas: 0.225 Mg/m3 / Density % sol: 53.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Crystals of A223-L208M were grown by hanging drop vapour diffusion using 2 micro-L of the protein solution and 2 micro-L in 0.1 M tri-sodium citrate dihydrate pH 5.6 and 35% t-butanol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.82653 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2009
Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11-h,-k,l20.499
ReflectionResolution: 1.82→50 Å / Num. obs: 47436 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.9
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 5 % / Rmerge(I) obs: 0.53 / Num. unique obs: 4662 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3J31

3j31


Resolution: 1.83→20.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.216 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.02 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19542 2466 5.3 %RANDOM
Rwork0.16364 ---
obs0.16534 44222 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.73 Å2
Baniso -1Baniso -2Baniso -3
1-17.19 Å20 Å20 Å2
2--17.19 Å20 Å2
3----34.37 Å2
Refinement stepCycle: 1 / Resolution: 1.83→20.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 0 51 3018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023046
X-RAY DIFFRACTIONr_bond_other_d0.0020.022905
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9684164
X-RAY DIFFRACTIONr_angle_other_deg0.72136688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8995390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.51126.446121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21915495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.118152
X-RAY DIFFRACTIONr_chiral_restr0.0770.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.70635951
X-RAY DIFFRACTIONr_sphericity_free8.878526
X-RAY DIFFRACTIONr_sphericity_bonded3.7155921
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
914medium positional0.150.5
1130loose positional3.875
582tight thermal1.870.5
914medium thermal2.912
1130loose thermal2.5610
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 173 -
Rwork0.217 3148 -
obs--99.67 %
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)
12.12480.0696-0.88911.5101-0.84593.0595-0.0070.0085-0.0297-0.0485-0.029-0.0880.10220.14380.0360.10960.0059-0.01630.112-0.01370.19038.339533.45229.6663
20.48162.92311.666318.446110.50415.9842-0.0567-0.0250.0313-0.15040.1098-0.0844-0.110.0673-0.05310.23470.0342-0.00050.1896-0.00350.2834.046154.363431.7781
32.1334-0.1823-0.17152.1488-0.76933.4219-0.02160.1430.0053-0.06740.03790.0330.1217-0.0671-0.01630.1046-0.0084-0.0120.11290.00230.1993-3.875772.02539.5732
42.4571-0.2175-0.88231.79550.62362.46820.00210.0947-0.0370.0041-0.02390.05520.0969-0.10840.02180.1161-0.0081-0.01610.12620.01360.1792-9.750731.898216.5832
50.3042-1.65971.099417.1653-11.39437.5637-0.2241-0.03720.05110.26360.46840.3582-0.1716-0.3205-0.24430.2933-0.0142-0.02810.157-0.00770.2717-7.171352.93812.7829
61.54430.2103-0.02141.89381.07773.44660.0235-0.0644-0.0243-0.02540.0307-0.05080.0790.1047-0.05420.12620.0079-0.0070.13720.00350.22512.919268.87356.3549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 131
2X-RAY DIFFRACTION2A132 - 140
3X-RAY DIFFRACTION3A141 - 223
4X-RAY DIFFRACTION4B19 - 131
5X-RAY DIFFRACTION5B132 - 140
6X-RAY DIFFRACTION6B141 - 223

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