[English] 日本語
Yorodumi
- PDB-7vws: Carbazole Prenyl Transferase LvqB4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vws
TitleCarbazole Prenyl Transferase LvqB4
ComponentsLvqB4
KeywordsTRANSFERASE / Prenyl transferase / Squalene synthase
Function / homologyChem-83B / Chem-AO6
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsSuemune, H. / Nagata, R. / Kuzuyama, T. / Nagano, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
Japan Society for the Promotion of Science (JSPS)19H05780 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Structural Basis for the Prenylation Reaction of Carbazole-Containing Natural Products Catalyzed by Squalene Synthase-Like Enzymes.
Authors: Nagata, R. / Suemune, H. / Kobayashi, M. / Shinada, T. / Shin-Ya, K. / Nishiyama, M. / Hino, T. / Sato, Y. / Kuzuyama, T. / Nagano, S.
History
DepositionNov 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Apr 3, 2024Group: 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: LvqB4
B: LvqB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,32110
Polymers82,0532
Non-polymers1,2688
Water12,376687
1
A: LvqB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6605
Polymers41,0261
Non-polymers6344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-19 kcal/mol
Surface area14990 Å2
MethodPISA
2
B: LvqB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6605
Polymers41,0261
Non-polymers6344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-19 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.240, 71.394, 83.894
Angle α, β, γ (deg.)90.000, 109.907, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein LvqB4


Mass: 41026.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AO6 / 2-methyl-1-[(2R)-2-oxidanylpropyl]-9H-carbazole-3,4-dione


Mass: 269.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-83B / [(3S)-3,7-dimethyloct-6-enyl] phosphono hydrogen phosphate


Mass: 316.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: PEG 3350

-
Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.999999 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 1.71→45.69 Å / Num. obs: 68798 / % possible obs: 89.46 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.09 Å2 / CC1/2: 0.913 / Net I/σ(I): 9.43
Reflection shellResolution: 1.71→1.771 Å / Num. unique obs: 18243 / CC1/2: 0.627

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-SAD

Resolution: 1.71→45.69 Å / SU ML: 0.2134 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2133 3378 4.97 %
Rwork0.1761 64627 -
obs0.1779 68005 89.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.05 Å2
Refinement stepCycle: LAST / Resolution: 1.71→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5215 0 82 687 5984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00645417
X-RAY DIFFRACTIONf_angle_d0.76127344
X-RAY DIFFRACTIONf_chiral_restr0.0451794
X-RAY DIFFRACTIONf_plane_restr0.0049946
X-RAY DIFFRACTIONf_dihedral_angle_d16.54081991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.3555840.2821500X-RAY DIFFRACTION50.03
1.73-1.760.3698730.30621658X-RAY DIFFRACTION54.62
1.76-1.780.8674800.84051327X-RAY DIFFRACTION55.18
1.79-1.820.53731200.57541766X-RAY DIFFRACTION63.08
1.82-1.850.2841140.21352179X-RAY DIFFRACTION73.45
1.85-1.880.27341220.2052569X-RAY DIFFRACTION83.96
1.88-1.920.251390.19642799X-RAY DIFFRACTION93.27
1.92-1.960.24871320.19042878X-RAY DIFFRACTION95.46
1.96-20.2231590.18032905X-RAY DIFFRACTION96.81
2-2.040.24461490.17992966X-RAY DIFFRACTION98.76
2.04-2.10.22281560.17392962X-RAY DIFFRACTION98.55
2.1-2.150.22041400.17012975X-RAY DIFFRACTION98.95
2.15-2.220.19211500.16352989X-RAY DIFFRACTION99.08
2.22-2.290.21221480.16512981X-RAY DIFFRACTION99.27
2.29-2.370.23011830.16982974X-RAY DIFFRACTION99.34
2.37-2.460.22981750.17122978X-RAY DIFFRACTION99.24
2.46-2.580.19311420.17732991X-RAY DIFFRACTION99.49
2.58-2.710.25711530.17673025X-RAY DIFFRACTION99.59
2.71-2.880.20931820.17442994X-RAY DIFFRACTION99.75
2.88-3.10.21061480.1773023X-RAY DIFFRACTION99.69
3.1-3.420.21961830.16232982X-RAY DIFFRACTION99.91
3.42-3.910.17151410.1483051X-RAY DIFFRACTION99.72
3.91-4.930.15371490.14883048X-RAY DIFFRACTION99.69
4.93-45.690.20731560.19183107X-RAY DIFFRACTION99.45
Refinement TLS params.Method: refined / Origin x: 8.29545145775 Å / Origin y: -16.0756513858 Å / Origin z: 20.4886773929 Å
111213212223313233
T0.192051284262 Å2-0.0321207098765 Å20.00864091630685 Å2-0.166094101703 Å2-0.00166735133397 Å2--0.137574730024 Å2
L0.320175586835 °2-0.289674599238 °20.0582814258145 °2-0.602898274972 °2-0.0857549978631 °2--0.244544976692 °2
S0.0252264607527 Å °0.0286084896305 Å °-0.0168881657128 Å °-0.042696503287 Å °-0.0432911234952 Å °0.0238166709197 Å °0.00541694000537 Å °0.00309382321024 Å °0.0195042715157 Å °
Refinement TLS groupSelection details: all

+
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