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- PDB-1sh3: Crystal Structure of Norwalk Virus Polymerase (MgSO4 crystal form) -

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Basic information

Entry
Database: PDB / ID: 1sh3
TitleCrystal Structure of Norwalk Virus Polymerase (MgSO4 crystal form)
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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / 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: 2.95 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: RNA Polymerase
B: RNA Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6764
Polymers113,6272
Non-polymers492
Water543
1
A: RNA Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8382
Polymers56,8141
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8382
Polymers56,8141
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.050, 109.140, 112.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASP6AA6 - 5076 - 507
21GLYGLYASPASP6BB6 - 5076 - 507
32MGMGMGMG1AC600
42MGMGMGMG1BD600

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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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ammonium sulfate, magnesium 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: Dec 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: 2.95→20 Å / Num. all: 27684 / Num. obs: 27684 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 16.7
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2688 / Rsym value: 0.618 / % possible all: 100
Reflection
*PLUS
Num. measured all: 185654
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 2688 / Num. measured obs: 18090

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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: 2.95→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.862 / SU B: 19.261 / SU ML: 0.354 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS refinement was performed for each of three domains in each protomer
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 1419 5.1 %RANDOM
Rwork0.21522 ---
obs0.21857 26218 100 %-
all-27637 --
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: 17.668 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2--1.85 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7887 0 2 3 7892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218092
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.96310977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77451003
X-RAY DIFFRACTIONr_chiral_restr0.0780.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026130
X-RAY DIFFRACTIONr_nbd_refined0.2170.23675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.27
X-RAY DIFFRACTIONr_mcbond_it0.89125027
X-RAY DIFFRACTIONr_mcangle_it1.6332.58138
X-RAY DIFFRACTIONr_scbond_it2.1623.53065
X-RAY DIFFRACTIONr_scangle_it3.3964.52839
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1tight positional0.070.05
3939loose positional0.615
1tight thermal0.170.5
3939loose thermal2.2510
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 99 -
Rwork0.292 1865 -
obs-1865 100 %
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)
11.7680.27650.32681.0046-0.19621.44520.0616-0.06580.08150.1187-0.01860.09750.01440.0806-0.04310.13610.0233-0.00970.0998-0.00040.000725.6481-1.428751.9046
23.4719-0.4291-0.1532.1957-1.42313.5571-0.05770.38480.0566-0.3128-0.1624-0.16350.07130.31810.22010.0681-0.0343-0.0080.19480.04240.049543.58492.340635.8839
31.27360.7058-1.27093.5695-3.08922.55780.1491-0.2320.226-0.00190.03720.2477-0.0773-0.0678-0.18630.18340.0118-0.02950.2840.00430.073716.83585.532423.9396
42.96540.49080.13162.72560.20862.17410.2344-0.2712-0.30190.1507-0.3546-0.6940.340.12990.12020.19320.0203-0.04170.14870.15430.349263.65035.31847.0719
54.15010.80350.60554.6733-1.21754.47850.29860.0999-0.2505-0.364-0.0697-1.41620.32440.5638-0.22890.1150.0475-0.06230.31990.25711.185986.911310.97872.9395
62.95435.81780.523710.4954-2.83090.5125-0.51650.3029-0.6024-1.33060.1069-0.68610.07630.12560.40960.77320.02630.31420.3928-0.17150.323370.703714.7922-21.4108
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 DIFFRACTION4BB6 - 2096 - 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: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.14
LS refinement shell
*PLUS
Rfactor Rfree: 0.387 / Rfactor Rwork: 0.286

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