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- PDB-2o1j: Structure of the extended diarrhea-inducing domain of rotavirus e... -

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Basic information

Entry
Database: PDB / ID: 2o1j
TitleStructure of the extended diarrhea-inducing domain of rotavirus enterotoxigenic protein NSP4
ComponentsNonstructural protein NSP4
KeywordsVIRAL PROTEIN / Rotavirus enterotoxin / Non structural protein / NSP4 / tetrameric coiled coil / Virulence
Function / homology
Function and homology information


: / toxin activity / membrane => GO:0016020 / induction by virus of host autophagy / extracellular region / metal ion binding
Similarity search - Function
Rotavirus non-structural protein 4 / Rotavirus non structural protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nonstructural protein NSP4
Similarity search - Component
Biological speciesRotavirus str.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSuguna, K. / Durga Rao, C. / Deepa, R.
CitationJournal: TO BE PUBLISHED
Title: Structure of the extended diarrhea-inducing domain of rotavirus enterotoxigenic protein NSP4
Authors: Deepa, R. / Durga Rao, C. / Suguna, K.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Nonstructural protein NSP4
B: Nonstructural protein NSP4
C: Nonstructural protein NSP4
D: Nonstructural protein NSP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4985
Polymers25,4584
Non-polymers401
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-97 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.614, 180.432, 48.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Nonstructural protein NSP4


Mass: 6364.456 Da / Num. of mol.: 4 / Fragment: diarrhea-inducing domain (residues 95-146)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus str. / Species: Rotavirus A / Strain: I321 / Gene: G10 / Plasmid: pET22b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 DE3 / References: UniProt: Q9PYC1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0M potassium sodium tetra hydrate, 0.1M HEPES, KOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 15, 2006 / Details: osmic mirror
RadiationMonochromator: CU Kalpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→37.8 Å / Num. obs: 5847 / % possible obs: 96.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.5 / Num. unique all: 833 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 201K

201k


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 33.786 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.863 / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31377 269 4.6 %RANDOM
Rwork0.24769 ---
obs0.25067 5545 94.49 %-
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: 20.091 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2---4.41 Å20 Å2
3---3.68 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 1 11 1340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9951786
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2724.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.68915271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4141511
X-RAY DIFFRACTIONr_chiral_restr0.1170.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02907
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.2730
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.2936
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7011.5902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25721380
X-RAY DIFFRACTIONr_scbond_it2.0333481
X-RAY DIFFRACTIONr_scangle_it3.644.5406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 11 -
Rwork0.335 385 -
obs--94.96 %
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)
13.194-8.4567-0.365739.82226.77693.403-0.2082-0.2913-0.14260.75240.4128-0.21810.11720.2369-0.20450.0538-0.0354-0.05620.2625-0.0270.057639.015126.53229.949
23.38188.57462.139570.272714.29894.3135-0.16040.1836-0.0419-0.54550.378-0.3940.01170.2227-0.21750.06720.0359-0.09540.18550.0013-0.070641.146125.56421.438
33.6375.8179-0.029228.5205-4.322.2097-0.02220.3527-0.4012-0.28230.4219-0.28960.209-0.2123-0.39970.13790.0034-0.0740.2866-0.12220.048632.629126.48119.764
43.9178-6.58672.308843.2512-9.64043.8934-0.3398-0.2835-0.22010.77310.48970.44490.0849-0.2914-0.14990.0215-0.05540.00830.197-0.0819-0.00330.512125.6528.332
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA95 - 1381 - 44
2X-RAY DIFFRACTION2BB95 - 1371 - 43
3X-RAY DIFFRACTION3CC95 - 1381 - 44
4X-RAY DIFFRACTION4DD95 - 1371 - 43

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