[English] 日本語
Yorodumi
- PDB-4jat: Crystal Structure of Mycobacterium tuberculosis PKS11 Reveals Int... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jat
TitleCrystal Structure of Mycobacterium tuberculosis PKS11 Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones
ComponentsAlpha-pyrone synthesis polyketide synthase-like Pks11
KeywordsTRANSFERASE / lipid biosynthesis / Structural Genomics / Enzyme Function Initiative / ketosynthase enzyme / Alkylpyrone synthesis / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


polyketide synthase complex / chalcone biosynthetic process / polyketide biosynthetic process / DIM/DIP cell wall layer assembly / lipid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Methyl-branched alkylpyrone synthesis polyketide synthase-like Pks11 / Methyl-branched alkylpyrone synthesis polyketide synthase-like Pks11
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsGokulan, K. / Sacchettini, J.C. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal structure of Mycobacterium tuberculosis polyketide synthase 11 (PKS11) reveals intermediates in the synthesis of methyl-branched alkylpyrones.
Authors: Gokulan, K. / O'Leary, S.E. / Russell, W.K. / Russell, D.H. / Lalgondar, M. / Begley, T.P. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-pyrone synthesis polyketide synthase-like Pks11
B: Alpha-pyrone synthesis polyketide synthase-like Pks11
C: Alpha-pyrone synthesis polyketide synthase-like Pks11
D: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6868
Polymers150,6604
Non-polymers1,0264
Water5,296294
1
A: Alpha-pyrone synthesis polyketide synthase-like Pks11
C: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8434
Polymers75,3302
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-16 kcal/mol
Surface area24190 Å2
MethodPISA
2
B: Alpha-pyrone synthesis polyketide synthase-like Pks11
D: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8434
Polymers75,3302
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-16 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.374, 48.871, 194.616
Angle α, β, γ (deg.)90.00, 97.95, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Alpha-pyrone synthesis polyketide synthase-like Pks11 / Alpha-pyrone synthesis polyketide synthase type III Pks11 / Chalcone synthase-like protein / CHS-like


Mass: 37665.078 Da / Num. of mol.: 4 / Mutation: C138S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: pks11, Rv1665, MT1705 / Production host: Mycobacterium smegmatis (bacteria)
References: UniProt: O06587, UniProt: P9WPF3*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M SODIUM ACETATE, 6% PEG 4K AND 10% ISOPROPANOL, pH 5.2, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.42→37.65 Å / Num. all: 51828 / Num. obs: 47290 / % possible obs: 96 % / Observed criterion σ(F): 13 / Observed criterion σ(I): 2.7

-
Processing

Software
NameClassification
HKL-2000data collection
MLPHAREphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→37.65 Å
RfactorNum. reflection% reflection
Rfree0.27626 2541 5.1 %
Rwork0.19598 --
obs0.20013 47290 96.5 %
all-51828 -
Refinement stepCycle: LAST / Resolution: 2.42→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10568 0 72 294 10934

+
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