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- PDB-1g1j: CRYSTAL STRUCTURE OF THE OLIGOMERIZATION DOMAIN FROM ROTAVIRUS NSP4 -

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Basic information

Entry
Database: PDB / ID: 1g1j
TitleCRYSTAL STRUCTURE OF THE OLIGOMERIZATION DOMAIN FROM ROTAVIRUS NSP4
ComponentsNON-STRUCTURAL GLYCOPROTEIN NSP4
KeywordsMETAL BINDING PROTEIN / NS28 / parallel coiled-coil / homo-tetramer / metal binding site / strontium / cation
Function / homology
Function and homology information


host caveola / host cell rough endoplasmic reticulum membrane / : / protein complex oligomerization / monoatomic ion channel activity / toxin activity / induction by virus of host autophagy / extracellular region / membrane / 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
STRONTIUM ION / Non-structural glycoprotein 4 / Non-structural glycoprotein 4
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.86 Å
AuthorsBowman, G.D. / Nodelman, I.M. / Schutt, C.E.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of the oligomerization domain of NSP4 from rotavirus reveals a core metal-binding site.
Authors: Bowman, G.D. / Nodelman, I.M. / Levy, O. / Lin, S.L. / Tian, P. / Zamb, T.J. / Udem, S.A. / Venkataraghavan, B. / Schutt, C.E.
History
DepositionOct 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NON-STRUCTURAL GLYCOPROTEIN NSP4
B: NON-STRUCTURAL GLYCOPROTEIN NSP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8963
Polymers10,8092
Non-polymers881
Water1,58588
1
A: NON-STRUCTURAL GLYCOPROTEIN NSP4
B: NON-STRUCTURAL GLYCOPROTEIN NSP4
hetero molecules

A: NON-STRUCTURAL GLYCOPROTEIN NSP4
B: NON-STRUCTURAL GLYCOPROTEIN NSP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7926
Polymers21,6174
Non-polymers1752
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8490 Å2
ΔGint-147 kcal/mol
Surface area10080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)34.917, 35.908, 60.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-201-

SR

21B-202-

HOH

DetailsThe biological assembly is a tetramer which can be generated from chains A and B by constructing symmetry mates across the two-fold.

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Components

#1: Protein/peptide NON-STRUCTURAL GLYCOPROTEIN NSP4


Mass: 5404.255 Da / Num. of mol.: 2 / Fragment: OLIGOMERIZATION DOMAIN / Source method: obtained synthetically
Details: This sequence is derived from NSP4 from Simian 11 rotavirus (strain SA11).
References: UniProt: O92323, UniProt: P04512*PLUS
#2: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.77 Å3/Da / Density % sol: 30.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG400, magnesium sulfate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMHEPES1drop
220-28 %PEG4001reservoir
3100 mMTris-HCl1reservoir
41reservoirSrCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9785,0.9788,0.95
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: May 12, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.97881
30.951
ReflectionResolution: 1.86→20 Å / Num. all: 138038 / Num. obs: 12450 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.3
Reflection shellResolution: 1.86→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.117 / % possible all: 100
Reflection
*PLUS
Num. measured all: 138038

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.86→19.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 711648.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Four water molecules have been modelled above the metal and hydrating water molecules. It is also possible that the four water molecules (two per ASU) are instead a small molecule lying ...Details: Four water molecules have been modelled above the metal and hydrating water molecules. It is also possible that the four water molecules (two per ASU) are instead a small molecule lying across the two-fold crystallographic axis. There are five residues whose side chains have alternative rotomer conformations and have been modelled as such: A98, A106, A112, B99, and B114.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1235 10.1 %RANDOM
Rwork0.216 ---
all0.218 12450 --
obs0.216 12259 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.74 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.44 Å20 Å20 Å2
2--2.81 Å20 Å2
3----11.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.86→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 1 88 809
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.432
X-RAY DIFFRACTIONc_mcangle_it1.982.5
X-RAY DIFFRACTIONc_scbond_it3.012.5
X-RAY DIFFRACTIONc_scangle_it4.53
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 187 9.6 %
Rwork0.252 1769 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it2.5
X-RAY DIFFRACTIONc_mcangle_it2.5
X-RAY DIFFRACTIONc_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.252

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