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- PDB-2bbd: Crystal Structure of the STIV MCP -

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Basic information

Entry
Database: PDB / ID: 2bbd
TitleCrystal Structure of the STIV MCP
Componentscoat protein
KeywordsVIRAL PROTEIN / Archaea / hyperthermophile / virus / evolution / crystal
Function / homology: / Sulfolobus turreted icosahedral virus 1-like, major capsid protein / viral capsid / Coat protein
Function and homology information
Biological speciesSulfolobus turreted icosahedral virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsKhayat, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses.
Authors: Khayat, R. / Tang, L. / Larson, E.T. / Lawrence, C.M. / Young, M. / Johnson, J.E.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: coat protein
B: coat protein
C: coat protein
D: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,98521
Polymers154,9764
Non-polymers2,00917
Water14,034779
1
A: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6899
Polymers38,7441
Non-polymers9458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8622
Polymers38,7441
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3356
Polymers38,7441
Non-polymers5915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0994
Polymers38,7441
Non-polymers3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)241.600, 82.890, 114.800
Angle α, β, γ (deg.)90.00, 116.00, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is believed to be a trimer. However, only monomers are observed in the ASU.

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Components

#1: Protein
coat protein


Mass: 38744.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus turreted icosahedral virus / Genus: Rudivirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q0J0
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 3.352 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 298.5 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 16% PEG 3350 10% MPD 0.2M Ammonium Citrate (pH 4.5) 5% (v/v) glycerol 2mM DTT 20mM N,N-Dimethyldecylamine-B-oxide 0.1M Bicine (pH 9.0), VAPOR DIFFUSION, HANGING DROP, temperature 298.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2004
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. all: 116333 / Num. obs: 114006 / % possible obs: 83.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.2 Å2
Reflection shellResolution: 2.04→2.17 Å / % possible all: 50

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→29.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 125966.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 6969 7 %RANDOM
Rwork0.207 ---
obs0.207 99205 76.4 %-
all-137645 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.0565 Å2 / ksol: 0.326427 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--13.2 Å20 Å2-6.41 Å2
2--12.56 Å20 Å2
3---0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.04→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9955 0 136 779 10870
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 762 7.1 %
Rwork0.267 10000 -
obs--50 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4mpd_xplor_par.txt

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