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- PDB-2vak: Crystal structure of the avian reovirus inner capsid protein sigmaA -

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Basic information

Entry
Database: PDB / ID: 2vak
TitleCrystal structure of the avian reovirus inner capsid protein sigmaA
ComponentsSIGMA A
KeywordsVIRAL PROTEIN / DOUBLE-STRANDED RNA BINDING / RNA
Function / homologySigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / viral capsid / Major inner capsid protein sigma 1
Function and homology information
Biological speciesAVIAN ORTHOREOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsGuardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / Hermo-Parrado, X.L. / Vazquez-Iglesias, L. / Martinez-Costas, J. / Benavente, J. / van Raaij, M.J.
Citation
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization of the Avian Reovirus Double-Stranded RNA-Binding and Core Protein Sigmaa
Authors: Hermo-Parrado, X.L. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / Vazquez-Iglesias, L. / Martinez-Costas, J. / Benavente, J. / van Raaij, M.J.
History
DepositionSep 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SIGMA A
B: SIGMA A
C: SIGMA A
D: SIGMA A
E: SIGMA A
F: SIGMA A
G: SIGMA A
H: SIGMA A
I: SIGMA A
J: SIGMA A
K: SIGMA A
L: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,95324
Polymers561,80012
Non-polymers1,15312
Water54,0993003
1
A: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
I: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
10
J: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
11
K: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
12
L: SIGMA A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9132
Polymers46,8171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.210, 129.909, 144.037
Angle α, β, γ (deg.)93.81, 105.05, 98.16
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SIGMA A


Mass: 46816.652 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN ORTHOREOVIRUS / Strain: S1133 / Plasmid: PMALC-S2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q9E6F8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3003 / 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: 3.2 Å3/Da / Density % sol: 62 %
Description: PDB ENTRY 1EJ6 CHAIN D WAS MODIFIED BY CHAINSAW BEFORE MOLECULAR REPLACEMENT
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 MM SODIUM CITRATE, SODIUM PHOSPHATE OR MES NAOH BUFFER PH 5.5 TO 6.5, 0.1 TO 0.6 M AMMONIUM SULPHATE 10 MM TRIS HCL, 1 MM EDTA SITTING DROP VAPOUR DIFFUSION AT 278 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.34→30 Å / Num. obs: 282973 / % possible obs: 94.3 % / Redundancy: 2 % / Biso Wilson estimate: 42.65 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.7
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 74.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0027refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EJ6

1ej6


Resolution: 2.34→29.85 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.919 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REFLECTIONS FOR CALCULATION OF RFREE WERE SELECTED IN THIN SHELLS BASED ON A PREVIOUS 2.5 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REFLECTIONS FOR CALCULATION OF RFREE WERE SELECTED IN THIN SHELLS BASED ON A PREVIOUS 2.5 A DATASET AND THEN EXTENDED TO THE NEW 2.34 ANGSTROM DATASET RANDOMLY
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1385 0.5 %RANDOM
Rwork0.21 ---
obs0.211 281587 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å2-1.61 Å2-0.77 Å2
2---0.6 Å20.77 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.34→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38161 0 60 3003 41224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02239213
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.93553538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0154867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47923.8511828
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.333155927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.15715276
X-RAY DIFFRACTIONr_chiral_restr0.0980.25798
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0230632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.219308
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.226560
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.23004
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.2134
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.236225041
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.115339275
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.102316674
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.249514263
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: 2.34→2.47 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 119 -
Rwork0.277 32494 -
obs--74.69 %

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