[English] 日本語
Yorodumi
- PDB-7vq9: Structure of MA1831 from Methanosarcina acetivorans in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vq9
TitleStructure of MA1831 from Methanosarcina acetivorans in complex with farnesyl thiopyrophosphate and isopentyl S-thiolodiphosphate
ComponentsDi-trans-poly-cis-decaprenylcistransferase
KeywordsTRANSFERASE / cis-prenyltransferase
Function / homology
Function and homology information


polyprenol biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / metal ion binding
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FPS / Chem-ISY / Di-trans-poly-cis-decaprenylcistransferase
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsZhang, L.L. / Chen, C.C. / Liu, W.D. / Huang, J.W. / Zhang, X.W. / Liu, B.B. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structural insights to a bi-functional isoprenyl diphosphate synthase that can catalyze head-to-tail and head-to-middle condensation.
Authors: Zhang, L. / Zhang, X. / Min, J. / Liu, B. / Huang, J.W. / Yang, Y. / Liu, W. / Dai, L. / Yang, Y. / Chen, C.C. / Guo, R.T.
History
DepositionOct 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Di-trans-poly-cis-decaprenylcistransferase
B: Di-trans-poly-cis-decaprenylcistransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,40312
Polymers51,6492
Non-polymers1,75410
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-93 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.899, 81.308, 60.023
Angle α, β, γ (deg.)90.000, 103.460, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Di-trans-poly-cis-decaprenylcistransferase


Mass: 25824.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) (archaea)
Gene: uppS, MA_1831 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TPS4

-
Non-polymers , 5 types, 411 molecules

#2: Chemical ChemComp-ISY / 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid / Isopentyl S-Thiolodiphosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.5M ammonium sulfate, 0.1M Tris (pH 8.0), 12% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.87→35.88 Å / Num. obs: 41757 / % possible obs: 98.7 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.02 / Rrim(I) all: 0.059 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.87-1.923.40.26770822530.9350.1560.3054.383
8.99-24.518.70.03633453840.9990.0130.03951.295.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CAQ

7caq


Resolution: 1.89→35.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.404 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2052 5.1 %RANDOM
Rwork0.1422 ---
obs0.1444 37927 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.27 Å2 / Biso mean: 23.398 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å2-0 Å2-0.06 Å2
2---0.06 Å2-0 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 1.89→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 98 401 3852
Biso mean--33.33 37.25 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133533
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173336
X-RAY DIFFRACTIONr_angle_refined_deg1.71.6574771
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5827710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83321.066197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32215617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7831526
X-RAY DIFFRACTIONr_chiral_restr0.090.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
LS refinement shellResolution: 1.89→1.939 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 127 -
Rwork0.189 2114 -
all-2241 -
obs--72.69 %

+
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