[English] 日本語
Yorodumi
- PDB-4amq: A Megaviridae Orfan gene encodes a new nucleotidyl transferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4amq
TitleA Megaviridae Orfan gene encodes a new nucleotidyl transferase
ComponentsL544
KeywordsTRANSFERASE / MIMIVIRUS / MG662 / TRANSCRIPTION COUPLED DNA REPAIR
Function / homology: / : / L544, nucleotidyltransferase domain / Nucleotidyl transferase L544, helical domain / virion component / : / Uncharacterized protein L544
Function and homology information
Biological speciesACANTHAMOEBA POLYPHAGA MIMIVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.17 Å
AuthorsLartigue, A. / Claverie, J.M. / Priet, S. / Abergel, C.
Citation
Journal: To be Published
Title: A Megaviridae Orphan Gene Encodes a New Nucleotidyl Transferase
Authors: Ciaccafava, A. / Lartigue, A. / Mansuelle, P. / Jeudy, S. / Abergel, C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Preliminary Crystallographic Analysis of a Possible Transcription Factor Encoded by the Mimivirus L544 Gene.
Authors: Ciaccafava, A. / Lartigue, A. / Mansuelle, P. / Jeudy, S. / Abergel, C.
History
DepositionMar 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L544
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4694
Polymers48,3351
Non-polymers1343
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.445, 91.092, 152.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

21A-2090-

HOH

31A-2098-

HOH

-
Components

#1: Protein L544


Mass: 48334.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACANTHAMOEBA POLYPHAGA MIMIVIRUS / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q5UQA5
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsMANGANESE (II) ION (MN): LOCATED IN THE NUCLEOTIDYL TRANSFERASE CATALYTIC DOMAIN
Sequence detailsADDITIONAL N-TERMINAL HIS-TAG, LEU -1 REPLACES INITIATION METHIONINE. NUCLEOTIDYL TRANSFERASE ...ADDITIONAL N-TERMINAL HIS-TAG, LEU -1 REPLACES INITIATION METHIONINE. NUCLEOTIDYL TRANSFERASE CATALYTIC DOMAIN IS RESIDUES 1-197.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growpH: 6
Details: PROTEIN CONCENTRATION: 10 MG/ML IN 10 MM CHES BUFFER PH 9.0 RESERVOIR: 4 TO 12% PEG 4000, 0.1 M SODIUM CACODYLATE BETWEEN PH 6 AND 7, 0.1 M MNCL2

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97918
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.17→50.4 Å / Num. obs: 20963 / % possible obs: 96 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.8
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.17→29.29 Å / SU ML: 0.31 / σ(F): 0.03 / Phase error: 25.6 / Stereochemistry target values: ML
Details: - LOOP RESIDUES 120 TO 126 ARE DISORDERED - LINKER RESIDUES 198 TO 210 ARE DISORDERED - RESIDUES 360 TO THE END ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2442 1088 5.2 %
Rwork0.2192 --
obs0.2206 20963 92.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.034 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.3615 Å20 Å20 Å2
2--1.4128 Å20 Å2
3----9.7743 Å2
Refinement stepCycle: LAST / Resolution: 2.17→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 3 122 2995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032926
X-RAY DIFFRACTIONf_angle_d0.6783949
X-RAY DIFFRACTIONf_dihedral_angle_d12.5631122
X-RAY DIFFRACTIONf_chiral_restr0.048448
X-RAY DIFFRACTIONf_plane_restr0.004489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1701-2.26880.29661340.24572371X-RAY DIFFRACTION89
2.2688-2.38840.27161240.24632394X-RAY DIFFRACTION90
2.3884-2.53790.28471340.23542475X-RAY DIFFRACTION93
2.5379-2.73380.32921390.23242529X-RAY DIFFRACTION94
2.7338-3.00860.26591410.24442494X-RAY DIFFRACTION94
3.0086-3.44340.26811480.22392538X-RAY DIFFRACTION94
3.4434-4.33610.21071310.19352535X-RAY DIFFRACTION93
4.3361-29.29290.2031370.20232539X-RAY DIFFRACTION90

+
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