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- PDB-1sh0: Crystal Structure of Norwalk Virus Polymerase (Triclinic) -

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Basic information

Entry
Database: PDB / ID: 1sh0
TitleCrystal Structure of Norwalk Virus Polymerase (Triclinic)
ComponentsRNA Polymerase
KeywordsTRANSFERASE / RNA POLYMERASE / VIRAL REPLICATION ENZYME
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent 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: 2.17 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
B: RNA Polymerase


Theoretical massNumber of molelcules
Total (without water)113,6272
Polymers113,6272
Non-polymers00
Water7,819434
1
A: RNA Polymerase


Theoretical massNumber of molelcules
Total (without water)56,8141
Polymers56,8141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA Polymerase


Theoretical massNumber of molelcules
Total (without water)56,8141
Polymers56,8141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.144, 59.914, 100.095
Angle α, β, γ (deg.)104.36, 92.49, 111.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein RNA Polymerase


Mass: 56813.551 Da / Num. of mol.: 2 / 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.: 434 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ammonium sulfate, Tris-Cl, glycerol, 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 15, 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: 2.17→40 Å / Num. all: 57284 / Num. obs: 57284 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 24.4
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5246 / Rsym value: 0.147 / % possible all: 86.9
Reflection
*PLUS
Num. measured all: 233635
Reflection shell
*PLUS
% possible obs: 86.9 % / Num. unique obs: 5246 / Num. measured obs: 7416

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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: 2.17→35.58 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.954 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.269 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS refinement was performed for each of three domains in each protomer.
RfactorNum. reflection% reflectionSelection details
Rfree0.25552 2892 5 %RANDOM
Rwork0.19412 ---
obs0.19716 54384 95.1 %-
all-54384 --
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: 21.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.71 Å2-0.94 Å2
2---0.08 Å2-1.65 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.17→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7887 0 0 434 8321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218091
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.96310977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26251003
X-RAY DIFFRACTIONr_chiral_restr0.0730.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026130
X-RAY DIFFRACTIONr_nbd_refined0.1920.23746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2505
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.214
X-RAY DIFFRACTIONr_mcbond_it1.17925027
X-RAY DIFFRACTIONr_mcangle_it1.9252.58138
X-RAY DIFFRACTIONr_scbond_it2.9983.53064
X-RAY DIFFRACTIONr_scangle_it4.1824.52839
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 183 -
Rwork0.215 3719 -
obs-3719 87 %
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)
10.4037-0.1434-0.22540.41280.09061.5709-0.0352-0.0197-0.0210.01670.0726-0.07880.17560.1873-0.03740.05960.03590.00140.04070.00340.0816-21.14119.678919.7073
23.0117-0.41551.50071.99270.07032.4219-0.14750.09320.353-0.18440.0738-0.1691-0.35040.1530.07370.0574-0.01310.01760.0036-0.0090.0442-30.017631.3926.289
32.5541-2.1778-1.65583.26392.08331.92970.01020.2221-0.2114-0.0146-0.25150.36110.0396-0.2820.24140.0794-0.0065-0.00420.08750.03230.118-38.865824.0323-0.6913
40.68430.17130.6370.17780.2012.3575-0.17760.07670.1998-0.0803-0.0117-0.0105-0.40840.18530.18920.1058-0.0399-0.02670.06860.02950.10756.74131.409360.3983
52.4860.3839-1.79561.62940.38633.3188-0.0991-0.2207-0.29410.2157-0.0081-0.08660.47120.07050.10720.09880.0018-0.0020.0825-0.00790.0591-2.26819.451454.7189
63.53711.07790.6471.39980.44080.2516-0.0946-0.0218-0.0558-0.067-0.01570.1283-0.0125-0.11860.11030.07420.00040.02150.07820.03510.0921-10.662317.261181.2876
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
6X-RAY DIFFRACTION4BB5 - 2095 - 209
7X-RAY DIFFRACTION4BB244 - 304244 - 304
8X-RAY DIFFRACTION5BB210 - 243210 - 243
9X-RAY DIFFRACTION5BB305 - 389305 - 389
10X-RAY DIFFRACTION6BB390 - 507390 - 507
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.02
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / Rfactor Rwork: 0.218

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