[English] 日本語
Yorodumi
- PDB-7ecd: Crystal structure of Tam41 from Firmicutes bacterium, complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ecd
TitleCrystal structure of Tam41 from Firmicutes bacterium, complex with CTP-Mg
ComponentsPhosphatidate cytidylyltransferase
KeywordsTRANSFERASE / CDP-DAG synthase / phosphatidic acid / cytidine-diphosphate diacylglycerol / Mitochondrial matrix
Function / homology
Function and homology information


phosphatidate cytidylyltransferase / phosphatidate cytidylyltransferase activity / CDP-diacylglycerol biosynthetic process / cardiolipin biosynthetic process / membrane
Similarity search - Function
Phosphatidate cytidylyltransferase, mitochondrial / Phosphatidate cytidylyltransferase, mitochondrial
Similarity search - Domain/homology
BROMIDE ION / CYTIDINE-5'-TRIPHOSPHATE / Phosphatidate cytidylyltransferase
Similarity search - Component
Biological speciesFirmicutes bacterium CAG:884 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKimura, K. / Kawai, F. / Kubota-Kawai, H. / Watanabe, Y. / Tamura, Y.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H06414 Japan
Japan Society for the Promotion of Science (JSPS)22227003 Japan
Japan Agency for Medical Research and Development (AMED)JP20gm5910026 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
CitationJournal: J.Biochem. / Year: 2022
Title: Crystal structure of Tam41 cytidine diphosphate diacylglycerol synthase from a Firmicutes bacterium.
Authors: Kimura, K. / Kawai, F. / Kubota-Kawai, H. / Watanabe, Y. / Tomii, K. / Kojima, R. / Hirata, K. / Yamamori, Y. / Endo, T. / Tamura, Y.
History
DepositionMar 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7155
Polymers32,0481
Non-polymers6674
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-13 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.159, 104.159, 113.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Phosphatidate cytidylyltransferase


Mass: 32047.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Firmicutes bacterium CAG:884 (bacteria)
Gene: BN804_00706 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: R5MX27, phosphatidate cytidylyltransferase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.82 Å3/Da / Density % sol: 74.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES ph 7.0, 13-15% (w/v) PEG 6000, 10% (v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 36822 / % possible obs: 99.7 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 23.8
Reflection shellResolution: 2.6→2.76 Å / Num. unique obs: 5901 / CC1/2: 0.722

-
Processing

Software
NameVersionClassification
PHENIX(1.17_3644: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→43.12 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 904 4.83 %
Rwork0.2008 --
obs0.2026 18728 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 32 2 2289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082334
X-RAY DIFFRACTIONf_angle_d1.0653141
X-RAY DIFFRACTIONf_dihedral_angle_d22.469311
X-RAY DIFFRACTIONf_chiral_restr0.055327
X-RAY DIFFRACTIONf_plane_restr0.005400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.41841440.35162962X-RAY DIFFRACTION99
2.76-2.970.27751570.27852924X-RAY DIFFRACTION100
2.97-3.270.31151330.25252987X-RAY DIFFRACTION100
3.27-3.750.26811760.21692948X-RAY DIFFRACTION100
3.75-4.720.22641430.17582983X-RAY DIFFRACTION100
4.72-43.120.18881510.17443020X-RAY DIFFRACTION100

+
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