[English] 日本語
Yorodumi
- PDB-1hi8: RNA dependent RNA polymerase from dsRNA bacteriophage phi6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hi8
TitleRNA dependent RNA polymerase from dsRNA bacteriophage phi6
ComponentsP2 PROTEIN
KeywordsRNA POLYMERASE / VIRAL POLYMERASE
Function / homology
Function and homology information


RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
Phage p2 RNA dependent RNA polymerase domain / Alpha-Beta Plaits - #1600 / Dihydrolipoamide Transferase / Dihydrolipoamide Transferase - #10 / Cystovirus, RNA-directed RNA polymerase, N-terminal / Cystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Other non-globular / Globin-like ...Phage p2 RNA dependent RNA polymerase domain / Alpha-Beta Plaits - #1600 / Dihydrolipoamide Transferase / Dihydrolipoamide Transferase - #10 / Cystovirus, RNA-directed RNA polymerase, N-terminal / Cystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Other non-globular / Globin-like / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase
Similarity search - Component
Biological speciesBACTERIOPHAGE PHI-6 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsGrimes, J.M. / Butcher, S.J. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I.
Citation
Journal: Nature / Year: 2001
Title: A Mechanism for Initiating RNA-Dependent RNA Polymerization
Authors: Butcher, S.J. / Grimes, J.M. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-Ray Crystallographic Studies on the Bacteriophage Phi6 RNA-Dependent RNA Polymerase
Authors: Butcher, S.J. / Makeyev, E.V. / Grimes, J.M. / Stuart, D.I. / Bamford, D.H.
History
DepositionJan 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 18, 2019Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P2 PROTEIN
B: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,2004
Polymers152,1512
Non-polymers492
Water00
1
A: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1002
Polymers76,0761
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1002
Polymers76,0761
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.000, 110.000, 159.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.86511, -0.4974, -0.06462), (-0.49976, 0.86575, 0.02663), (0.0427, 0.05533, -0.99755)
Vector: 92.69189, 38.53016, 177.2426)

-
Components

#1: Protein P2 PROTEIN / RNA-DIRECTED RNA POLYMERASE


Mass: 76075.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE PHI-6 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11124
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Compound detailsP2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID. IT IS RESPONSIBLE FOR GENOMIC ...P2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID. IT IS RESPONSIBLE FOR GENOMIC REPLICATION AND TRANSCRIPTION.
Sequence detailsERROR IN RESIDUE 456 IN SWISS PROT THE RESIDUE IS MET

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 67 %
Crystal growpH: 6.7
Details: 1:1 PROTEIN(5MG/ML):WELL WELL SOLUTION: 10% PEG 8000, 0.1M MES, 2 MM MNCL2, pH 6.70
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: Butcher, S.J., (2000) Acta Crystallogr.,Sect.D, 56, 1473.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 %PEG80001reservoir
30.1 MMES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923, 0.97939, 0.99988, 0.92873
DetectorType: SBC / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979391
30.999881
40.928731
ReflectionResolution: 2.5→50 Å / Num. obs: 66000 / % possible obs: 88 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.4 / % possible all: 15
Reflection
*PLUS
Num. measured all: 430000
Reflection shell
*PLUS
% possible obs: 66 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.316 3339 4.5 %RANDOM
Rwork0.28 ---
obs0.28 65827 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1--10.2 Å2-10.4 Å20 Å2
2---10.2 Å20 Å2
3---20.5 Å2
Refine analyzeLuzzati d res low obs: 50 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10530 0 2 0 10532
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it113
X-RAY DIFFRACTIONc_mcangle_it124
X-RAY DIFFRACTIONc_scbond_it164
X-RAY DIFFRACTIONc_scangle_it175
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM

+
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://pdbjlvh1.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