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- PDB-3f2e: Crystal structure of Yellowstone SIRV coat protein C-terminus -

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Basic information

Entry
Database: PDB / ID: 3f2e
TitleCrystal structure of Yellowstone SIRV coat protein C-terminus
ComponentsSIRV coat protein
KeywordsVIRAL PROTEIN / four helix bundle / virus coat protein
Function / homologySulfolobus virus, coat protein, C-terminal / Sulfolobus virus coat protein C terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #800 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / CITRIC ACID / SIRV coat protein
Function and homology information
Biological speciesSulfolobus islandicus rudivirus 1 variant YNP
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.668 Å
AuthorsTaurog, R.E. / Szymczyna, B.R. / Williamson, J.R. / Johnson, J.E.
CitationJournal: Structure / Year: 2009
Title: Synergy of NMR, computation, and X-ray crystallography for structural biology.
Authors: Szymczyna, B.R. / Taurog, R.E. / Young, M.J. / Snyder, J.C. / Johnson, J.E. / Williamson, J.R.
History
DepositionOct 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIRV coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6912
Polymers10,4991
Non-polymers1921
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.410, 54.410, 77.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SIRV coat protein


Mass: 10498.848 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Details: pET31a tags were removed from the vector, a C-terminal hexahistidine tag was cloned in
Source: (gene. exp.) Sulfolobus islandicus rudivirus 1 variant YNP
Plasmid: pET31a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLySs / References: UniProt: D0VX05*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop
Details: SIRV CP (residues 46-134) at 19 or 30 mg/ml in 20 mM Na MES pH 6.0 was mixed 1:1 with 25% PEG 20,000, 0.1 M Na Citrate pH 3.6, 4-9% sucrose. Crystals were frozen in of 14% PEG 20,000, 50 mM ...Details: SIRV CP (residues 46-134) at 19 or 30 mg/ml in 20 mM Na MES pH 6.0 was mixed 1:1 with 25% PEG 20,000, 0.1 M Na Citrate pH 3.6, 4-9% sucrose. Crystals were frozen in of 14% PEG 20,000, 50 mM sodium citrate pH 3.6, 15-25% sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.668→44.588 Å / Num. obs: 14062 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 16.8 % / Biso Wilson estimate: 24.675 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.062 / Net I/σ(I): 33.4
Reflection shellResolution: 1.668→1.7 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 8.27 / Num. unique all: 965 / Rsym value: 0.371 / % possible all: 94.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CS-Rosetta model

Resolution: 1.668→31.642 Å / SU ML: 0.14 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 703 5 %random
Rwork0.1837 ---
obs0.1846 14055 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.566 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.2583 Å2-0 Å2-0 Å2
2---0.2583 Å20 Å2
3----5.774 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: LAST / Resolution: 1.668→31.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms600 0 13 80 693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_deg0.833
X-RAY DIFFRACTIONf_dihedral_angle_d15.532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.668-1.79710.23131340.1832541254197
1.7971-1.97790.19541380.17532623262399
1.9779-2.26410.17781400.163926572657100
2.2641-2.85220.17711420.179226912691100
2.8522-31.64740.21841490.18728402840100

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