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- PDB-1sh2: Crystal Structure of Norwalk Virus Polymerase (Metal-free, Center... -

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Basic information

Entry
Database: PDB / ID: 1sh2
TitleCrystal Structure of Norwalk Virus Polymerase (Metal-free, Centered Orthorhombic)
ComponentsRNA Polymerase
KeywordsTRANSFERASE / RNA POLYMERASE / VIRAL ENZYME / VIRAL REPLICATION
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / host cell / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helix non-globular / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNg, K.K. / Pendas-Franco, N. / Rojo, J. / Boga, J.A. / Machin, A. / Alonso, J.M. / Parra, F.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of norwalk virus polymerase reveals the carboxyl terminus in the active site cleft.
Authors: Ng, K.K. / Pendas-Franco, N. / Rojo, J. / Boga, J.A. / Machin, A. / Alonso, J.M. / Parra, F.
History
DepositionFeb 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA Polymerase


Theoretical massNumber of molelcules
Total (without water)56,8141
Polymers56,8141
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.270, 115.240, 91.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

21A-649-

HOH

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Components

#1: Protein RNA Polymerase


Mass: 56813.551 Da / Num. of mol.: 1 / Fragment: C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Genus: Norovirus / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue / References: UniProt: Q70ET3, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ammonium sulfate, Tris-Cl, glycerol, CHAPS, 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlpolymerase1drop
224 %(w/v)PEG80001reservoir
3100-200 mMammonium sulfate1reservoir
450 mMTris-Cl1reservoirpH7.5
515 %(w/v)glycerol1reservoir
60.2 %(w/v)CHAPS1reservoir
714 mM2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2003 / Details: Mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 27003 / Num. obs: 27003 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 19.8
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2054 / Rsym value: 0.402 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 215719
Reflection shell
*PLUS
% possible obs: 91.3 % / Num. unique obs: 2054 / Num. measured obs: 7221

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KHV

1khv


Resolution: 2.3→36.04 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.887 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.357 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS refinement was performed for each of three domains
RfactorNum. reflection% reflectionSelection details
Rfree0.29087 1596 5.9 %RANDOM
Rwork0.22672 ---
obs0.23054 25374 100 %-
all-25374 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---5.55 Å20 Å2
3---5.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 0 139 4078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214041
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9635483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5095501
X-RAY DIFFRACTIONr_chiral_restr0.0770.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023063
X-RAY DIFFRACTIONr_nbd_refined0.1940.21835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.24
X-RAY DIFFRACTIONr_mcbond_it0.99122511
X-RAY DIFFRACTIONr_mcangle_it1.84444065
X-RAY DIFFRACTIONr_scbond_it2.3941530
X-RAY DIFFRACTIONr_scangle_it3.23851418
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.347 113
Rwork0.289 1691
obs-1691
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)
12.22960.0347-0.36513.8015-0.05920.53630.01070.1684-0.2669-0.2143-0.02330.3148-0.05070.02350.01260.2175-0.0096-0.04160.2575-0.02210.015125.006195.986143.905
24.2108-1.5011.13765.5107-0.04922.2852-0.00550.2057-0.7324-0.2515-0.0156-0.27820.09380.29120.02110.2068-0.03890.02590.2153-0.0280.285335.69474.07343.9947
33.1289-2.06131.64125.2192-1.99032.7242-0.2131-0.30440.22060.63480.0479-0.3378-0.3703-0.15680.16520.24140.0108-0.02780.3725-0.00870.418954.534694.873151.1468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 2096 - 209
2X-RAY DIFFRACTION1AA244 - 304244 - 304
3X-RAY DIFFRACTION2AA210 - 243210 - 243
4X-RAY DIFFRACTION2AA305 - 389305 - 389
5X-RAY DIFFRACTION3AA390 - 507390 - 507
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.08
LS refinement shell
*PLUS
Rfactor Rfree: 0.344 / Rfactor Rwork: 0.291

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