[English] 日本語
Yorodumi
- PDB-6vpt: Crystal structure and mechanistic molecular modeling studies of R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vpt
TitleCrystal structure and mechanistic molecular modeling studies of Rv3377c: the Mycobacterium tuberculosis diterpene cyclase
ComponentsCyclase
KeywordsLYASE / diterpene synthase / diterpene cyclase
Function / homology
Function and homology information


halimadienyl-diphosphate synthase / geranylgeranyl diphosphate metabolic process / halimadienyl-diphosphate synthase activity / tuberculosinol biosynthetic process / diterpenoid biosynthetic process / cellular response to magnesium starvation / response to host immune response / terpene synthase activity / isomerase activity / lyase activity / magnesium ion binding
Similarity search - Function
Glycosyltransferase - #160 / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / : / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Cyclase / Type B diterpene cyclase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.718 Å
AuthorsZhang, T. / Prach, L. / DiMaio, F. / Siegel, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1827246,1805510,1627539,CHE-1565933,CHE-030089 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM076324, P42ES004699 United States
CitationJournal: Biochemistry / Year: 2020
Title: Crystal Structure and Mechanistic Molecular Modeling Studies of Mycobacterium tuberculosis Diterpene Cyclase Rv3377c.
Authors: Zhang, Y. / Prach, L.M. / O'Brien, T.E. / DiMaio, F. / Prigozhin, D.M. / Corn, J.E. / Alber, T. / Siegel, J.B. / Tantillo, D.J.
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclase


Theoretical massNumber of molelcules
Total (without water)55,3241
Polymers55,3241
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.900, 76.428, 50.123
Angle α, β, γ (deg.)90.000, 91.640, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Cyclase / Type B diterpene cyclase


Mass: 55324.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: ERS023446_02740, EZX46_08560, FDK60_02635, FDK62_05385, SAMEA2682864_03253, SAMEA2683035_03439
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045JBW1, UniProt: O50406*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 20% polyethylene glycol (PEG) 8000 and 0.1 M (cyclohexylamino) ethanesulfonic acid (CHES) pH 9.5 with 2 mM MgCl

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.718→50 Å / Num. obs: 12602 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 47.05 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.8
Reflection shellResolution: 2.718→2.99 Å / Rmerge(I) obs: 0.421 / Num. unique obs: 2974 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pya

3pya


Resolution: 2.718→40.015 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.46
RfactorNum. reflection% reflection
Rfree0.2393 611 4.85 %
Rwork0.2138 --
obs0.2151 12602 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.8 Å2 / Biso mean: 45.793 Å2 / Biso min: 18.36 Å2
Refinement stepCycle: final / Resolution: 2.718→40.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 0 32 3789
Biso mean---39.59 -
Num. residues----483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7182-2.99170.33951490.2805282594
2.9917-3.42440.28351470.24273029100
3.4244-4.31360.23341700.23032100
4.3136-40.0150.1941450.19293105100

+
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