[English] 日本語
Yorodumi
- PDB-2jlf: STRUCTURAL EXPLANATION FOR THE ROLE OF MN IN THE ACTIVITY OF PHI6... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jlf
TitleSTRUCTURAL EXPLANATION FOR THE ROLE OF MN IN THE ACTIVITY OF PHI6 RNA- DEPENDENT RNA POLYMERASE
ComponentsRNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE / RNA-DIRECTED RNA POLYMERASE / METAL-BINDING / RNA POLYMERASE / RNA REPLICATION / VIRION / MANGANESE / MAGNESIUM / VIRAL POLYMERASE / NUCLEOTIDE-BINDING
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 speciesPSEUDOMONAS PHAGE PHI6 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPoranen, M.M. / Salgado, P.S. / Koivunen, M.R.L. / Wright, S. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structural Explanation for the Role of Mn2+ in the Activity of {Phi}6 RNA-Dependent RNA Polymerase.
Authors: Poranen, M.M. / Salgado, P.S. / Koivunen, M.R.L. / Wright, S. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
History
DepositionSep 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-DIRECTED RNA POLYMERASE
B: RNA-DIRECTED RNA POLYMERASE
C: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,8175
Polymers224,7073
Non-polymers1102
Water00
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9572
Polymers74,9021
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9572
Polymers74,9021
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)74,9021
Polymers74,9021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.040, 110.040, 159.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 3:30 OR RESSEQ 104:276 OR RESSEQ 333:397 )
211CHAIN B AND (RESSEQ 3:30 OR RESSEQ 104:276 OR RESSEQ 333:397 )
311CHAIN C AND (RESSEQ 3:30 OR RESSEQ 104:276 OR RESSEQ 333:397 )
112CHAIN A AND (RESSEQ 277:332 OR RESSEQ 398:517 )
212CHAIN B AND (RESSEQ 277:332 OR RESSEQ 398:517 )
312CHAIN C AND (RESSEQ 277:332 OR RESSEQ 398:517 )
113CHAIN A AND (RESSEQ 37:91 OR RESSEQ 518:600 )
213CHAIN B AND (RESSEQ 37:91 OR RESSEQ 518:600 )
313CHAIN C AND (RESSEQ 37:91 OR RESSEQ 518:600 )
114CHAIN A AND (RESSEQ 601:663 )
214CHAIN B AND (RESSEQ 601:663 )
314CHAIN C AND (RESSEQ 601:663 )

NCS ensembles :
ID
1
2
3
4

-
Components

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


Mass: 74902.219 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-665 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI6 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P11124, RNA-directed RNA polymerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 492 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 492 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 492 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 492 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 492 TO GLN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.3 % / Description: NONE
Crystal growDetails: 15-20% POLYETHYLENE GLYCOL 4000, 8.5% ISOPROPANOL, 15% GLYCEROL AND 100MM HEPES, PH 7.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.89
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 52552 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 41.42 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHS

1hhs


Resolution: 3.2→18.021 Å / SU ML: 0.56 / σ(F): 1.97 / Phase error: 27.82 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE NOT BUILT
RfactorNum. reflection% reflection
Rfree0.286 1771 5.02 %
Rwork0.2275 --
obs0.2304 35309 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.207 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9081 Å2-0 Å20 Å2
2---0.9081 Å20 Å2
3---1.8162 Å2
Refinement stepCycle: LAST / Resolution: 3.2→18.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15608 0 2 0 15610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d015996
X-RAY DIFFRACTIONf_angle_d1.0821640
X-RAY DIFFRACTIONf_dihedral_angle_d16.565864
X-RAY DIFFRACTIONf_chiral_restr0.072279
X-RAY DIFFRACTIONf_plane_restr02821
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2053X-RAY DIFFRACTIONPOSITIONAL
12B2053X-RAY DIFFRACTIONPOSITIONAL0.068
13C2053X-RAY DIFFRACTIONPOSITIONAL0.054
21A1412X-RAY DIFFRACTIONPOSITIONAL
22B1412X-RAY DIFFRACTIONPOSITIONAL0.059
23C1412X-RAY DIFFRACTIONPOSITIONAL0.063
31A1140X-RAY DIFFRACTIONPOSITIONAL
32B1140X-RAY DIFFRACTIONPOSITIONAL0.046
33C1140X-RAY DIFFRACTIONPOSITIONAL0.058
41A446X-RAY DIFFRACTIONPOSITIONAL
42B446X-RAY DIFFRACTIONPOSITIONAL0.046
43C442X-RAY DIFFRACTIONPOSITIONAL0.033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.28610.38421590.31512573X-RAY DIFFRACTION100
3.2861-3.38220.3681220.29712582X-RAY DIFFRACTION100
3.3822-3.49060.32971300.26972594X-RAY DIFFRACTION100
3.4906-3.61440.29831470.26052571X-RAY DIFFRACTION100
3.6144-3.75790.3181560.23192544X-RAY DIFFRACTION100
3.7579-3.92720.32171380.23462620X-RAY DIFFRACTION100
3.9272-4.13190.30561400.22412577X-RAY DIFFRACTION100
4.1319-4.38730.2811230.20652589X-RAY DIFFRACTION100
4.3873-4.72040.21591510.18442574X-RAY DIFFRACTION100
4.7204-5.18520.22271210.18382595X-RAY DIFFRACTION100
5.1852-5.91220.26211480.19632582X-RAY DIFFRACTION100
5.9122-7.36320.22461210.18832598X-RAY DIFFRACTION100
7.3632-18.02080.17921150.16762539X-RAY DIFFRACTION98

+
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