[English] 日本語
Yorodumi
- PDB-1sh0: Crystal Structure of Norwalk Virus Polymerase (Triclinic) -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 2.17 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more