[English] 日本語
Yorodumi
- PDB-5guf: Structural insight into an intramembrane enzyme for archaeal memb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5guf
TitleStructural insight into an intramembrane enzyme for archaeal membrane lipids biosynthesis
ComponentsCDP-archaeol synthase
KeywordsTRANSFERASE / membrane protein / cars
Function / homology
Function and homology information


CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol synthase / CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase activity / glycerophospholipid biosynthetic process / plasma membrane => GO:0005886
Similarity search - Function
CDP-archaeol synthase, archaea / CDP-archaeol synthase / CDP-archaeol synthase
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / : / CDP-archaeol synthase
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.397 Å
AuthorsCheng, W. / Ren, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570842 China
CitationJournal: Cell Res. / Year: 2017
Title: Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes.
Authors: Ren, S. / Caforio, A. / Yang, Q. / Sun, B. / Yu, F. / Zhu, X. / Wang, J. / Dou, C. / Fu, Q. / Huang, N. / Sun, Q. / Nie, C. / Qi, S. / Gong, X. / He, J. / Wei, Y. / Driessen, A.J. / Cheng, W.
History
DepositionAug 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CDP-archaeol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6366
Polymers19,0401
Non-polymers5955
Water1,33374
1
A: CDP-archaeol synthase
hetero molecules

A: CDP-archaeol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,27112
Polymers38,0812
Non-polymers1,19010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3960 Å2
ΔGint-66 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.505, 89.249, 98.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

-
Components

#1: Protein CDP-archaeol synthase / CDP-2 / 3-bis-(O-geranylgeranyl)-sn-glycerol synthase


Mass: 19040.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: carS, APE_0433
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9YF05, CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol synthase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.27 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 200mM NaCl, 20% (w/v) PEG 400, 100mM Tris/HCl pH 8.0

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9973 Å
DetectorType: DECTRIS PILATUS 300K / Detector: CCD / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9973 Å / Relative weight: 1
ReflectionResolution: 2.38→47.7 Å / Num. obs: 9961 / % possible obs: 98.5 % / Redundancy: 10.2 % / Biso Wilson estimate: 37.701436451 Å2 / Net I/σ(I): 24.4

-
Processing

Software
NameVersionClassification
PHENIX(dev_2719)refinement
HKL-3000data processing
Aimlessdata reduction
XDSdata extraction
RefinementResolution: 2.397→44.625 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 995 9.99 %
Rwork0.2072 --
obs0.2114 9958 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.397→44.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 33 74 1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021186
X-RAY DIFFRACTIONf_angle_d0.9941625
X-RAY DIFFRACTIONf_dihedral_angle_d11.496940
X-RAY DIFFRACTIONf_chiral_restr0.051199
X-RAY DIFFRACTIONf_plane_restr0.007205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3968-2.52320.30781250.23461148X-RAY DIFFRACTION90
2.5232-2.68130.25551470.20891258X-RAY DIFFRACTION99
2.6813-2.88830.25231320.19321281X-RAY DIFFRACTION100
2.8883-3.17880.21861410.18141297X-RAY DIFFRACTION100
3.1788-3.63860.19481500.1771294X-RAY DIFFRACTION100
3.6386-4.58360.26041460.19571312X-RAY DIFFRACTION100
4.5836-44.63220.26991540.24441373X-RAY DIFFRACTION99

+
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