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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jao
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
(2S)-2-methylheptadecan-1-ol / 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 / MAD / Resolution: 2.05 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 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,7788
Polymers150,7254
Non-polymers1,0544
Water6,936385
1
D: Alpha-pyrone synthesis polyketide synthase-like Pks11
C: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8894
Polymers75,3622
Non-polymers5272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-17 kcal/mol
Surface area23090 Å2
MethodPISA
2
B: Alpha-pyrone synthesis polyketide synthase-like Pks11
A: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8894
Polymers75,3622
Non-polymers5272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-16 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.123, 48.426, 189.694
Angle α, β, γ (deg.)90.00, 97.25, 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: 37681.145 Da / Num. of mol.: 4
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


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-JAO / (2S)-2-methylheptadecan-1-ol


Mass: 270.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M sodium acetate trihydrate, 5.6% PEG 4000, 10% isopropanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979, 0.97179
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.971791
ReflectionResolution: 2.05→47.04 Å / Num. obs: 63039 / % possible obs: 92 % / Observed criterion σ(F): 11.66 / Observed criterion σ(I): 6.39

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→47.04 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 34.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 3158 5.01 %
Rwork0.211 --
obs0.214 63025 77 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.05 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4375 Å2-0 Å2-5.7154 Å2
2---2.7344 Å2-0 Å2
3----1.7031 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10568 0 74 385 11027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910852
X-RAY DIFFRACTIONf_angle_d1.32714766
X-RAY DIFFRACTIONf_dihedral_angle_d18.8313994
X-RAY DIFFRACTIONf_chiral_restr0.0861726
X-RAY DIFFRACTIONf_plane_restr0.0051924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07590.2701220.2925426X-RAY DIFFRACTION13
2.0759-2.10840.4115530.29181128X-RAY DIFFRACTION33
2.1084-2.14290.3443530.30481219X-RAY DIFFRACTION37
2.1429-2.17990.3601650.291346X-RAY DIFFRACTION40
2.1799-2.21950.3441870.28771521X-RAY DIFFRACTION45
2.2195-2.26220.3302970.27551835X-RAY DIFFRACTION55
2.2622-2.30840.3561910.25982044X-RAY DIFFRACTION60
2.3084-2.35860.33451300.28372140X-RAY DIFFRACTION65
2.3586-2.41340.32491430.26832455X-RAY DIFFRACTION73
2.4134-2.47380.3891410.27172660X-RAY DIFFRACTION80
2.4738-2.54070.35251430.27052961X-RAY DIFFRACTION86
2.5407-2.61540.32261570.26653115X-RAY DIFFRACTION94
2.6154-2.69980.29481480.25953303X-RAY DIFFRACTION97
2.6998-2.79630.32131510.25583292X-RAY DIFFRACTION97
2.7963-2.90830.31411660.24873263X-RAY DIFFRACTION97
2.9083-3.04060.29891980.24313299X-RAY DIFFRACTION97
3.0406-3.20090.29511820.22773343X-RAY DIFFRACTION99
3.2009-3.40140.31831860.21213336X-RAY DIFFRACTION99
3.4014-3.66390.26111840.20023382X-RAY DIFFRACTION100
3.6639-4.03240.2631850.17663412X-RAY DIFFRACTION100
4.0324-4.61550.21591800.15283399X-RAY DIFFRACTION100
4.6155-5.81330.23811930.18643444X-RAY DIFFRACTION100
5.8133-47.040.21192030.18313544X-RAY DIFFRACTION100

+
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