[English] 日本語
Yorodumi
- PDB-9c1d: Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c1d
TitleMycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO
ComponentsPolyketide synthase Pks13
KeywordsANTIBIOTIC / inhibitor / covalent / SuFEx / acyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTang, S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Welch FoundationA-0015 United States
Bill & Melinda Gates FoundationINV-040487 United States
CitationJournal: Nature / Year: 2025
Title: SuFEx-based antitubercular compound irreversibly inhibits Pks13.
Authors: Krieger, I.V. / Sukheja, P. / Yang, B. / Tang, S. / Selle, D. / Woods, A. / Engelhart, C. / Kumar, P. / Harbut, M.B. / Liu, D. / Tsuda, B. / Qin, B. / Bare, G.A.L. / Li, G. / Chi, V. / ...Authors: Krieger, I.V. / Sukheja, P. / Yang, B. / Tang, S. / Selle, D. / Woods, A. / Engelhart, C. / Kumar, P. / Harbut, M.B. / Liu, D. / Tsuda, B. / Qin, B. / Bare, G.A.L. / Li, G. / Chi, V. / Gambacurta, J. / Hvizdos, J. / Reagan, M. / Jones, I.L. / Massoudi, L.M. / Woolhiser, L.K. / Cascioferro, A. / Kundrick, E. / Singh, P. / Reiley, W. / Ioerger, T.R. / Kandula, D.R. / McCabe, J.W. / Guo, T. / Alland, D. / Boshoff, H.I. / Schnappinger, D. / Robertson, G.T. / Mdluli, K. / Lee, K.J. / Dong, J. / Li, S. / Schultz, P.G. / Joseph, S.B. / Love, M.S. / Sharpless, K.B. / Petrassi, H.M. / Chatterjee, A.K. / Sacchettini, J.C. / McNamara, C.W.
History
DepositionMay 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 13, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 1, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyketide synthase Pks13
B: Polyketide synthase Pks13
C: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,13760
Polymers159,2243
Non-polymers4,91357
Water9,386521
1
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,86933
Polymers53,0751
Non-polymers2,79432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-64 kcal/mol
Surface area19780 Å2
MethodPISA
2
B: Polyketide synthase Pks13
C: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,26827
Polymers106,1502
Non-polymers2,11925
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-69 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.183, 106.183, 259.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-1104-

SO4

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Polyketide synthase Pks13


Mass: 53074.770 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pks13, Rv3800c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

-
Non-polymers , 10 types, 578 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.8 M (NH)4SO4, 4%-6% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 93969 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.027 / Rrim(I) all: 0.096 / Χ2: 0.959 / Net I/σ(I): 5.9 / Num. measured all: 1139148
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.05-2.0911.40.99146580.8630.9630.2951.0350.734100
2.09-2.1211.90.79546130.9220.980.2330.8290.746100
2.12-2.1612.10.73946110.9460.9860.2170.7710.746100
2.16-2.2112.20.62446310.950.9870.1830.6510.739100
2.21-2.26120.51446290.9640.9910.1530.5360.771100
2.26-2.31110.46646380.9610.990.1450.4880.776100
2.31-2.3712.20.39846050.9770.9940.1170.4150.787100
2.37-2.4312.60.34846540.980.9950.10.3630.802100
2.43-2.512.50.29546670.9850.9960.0850.3070.826100
2.5-2.5812.30.24546450.9880.9970.0710.2550.848100
2.58-2.6812.10.21446470.9910.9980.0630.2230.872100
2.68-2.7811.60.17946760.9920.9980.0540.1870.92399.9
2.78-2.9111.70.14146690.9950.9990.0420.1470.986100
2.91-3.0612.50.11247040.9970.9990.0320.1171.046100
3.06-3.2512.50.0947050.9980.9990.0260.0941.125100
3.25-3.5112.40.07347130.99810.0220.0771.243100
3.51-3.8611.80.06247480.99810.0190.0641.34100
3.86-4.4213.10.05348010.99810.0150.0551.347100
4.42-5.5612.20.04948320.99910.0150.0521.22799.9
5.56-5012.40.04451230.99910.0130.0461.15999.9

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→49.14 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 2757 2.96 %
Rwork0.1914 --
obs0.1923 93267 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7170 0 291 521 7982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.569
X-RAY DIFFRACTIONf_dihedral_angle_d13.0452756
X-RAY DIFFRACTIONf_chiral_restr0.0421141
X-RAY DIFFRACTIONf_plane_restr0.0061324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.34621360.29454381X-RAY DIFFRACTION97
2.08-2.120.29851320.25784393X-RAY DIFFRACTION98
2.12-2.160.26731330.23814420X-RAY DIFFRACTION99
2.16-2.210.23721370.22964430X-RAY DIFFRACTION99
2.21-2.260.24491350.21284449X-RAY DIFFRACTION99
2.26-2.310.22821340.21364469X-RAY DIFFRACTION99
2.31-2.370.22011370.21324427X-RAY DIFFRACTION99
2.37-2.430.22841320.21244485X-RAY DIFFRACTION99
2.43-2.50.2551410.2174495X-RAY DIFFRACTION99
2.5-2.580.24741380.21744480X-RAY DIFFRACTION99
2.58-2.670.24881330.21044491X-RAY DIFFRACTION100
2.67-2.780.2481330.20394539X-RAY DIFFRACTION100
2.78-2.910.22981440.20584506X-RAY DIFFRACTION100
2.91-3.060.2591380.21194555X-RAY DIFFRACTION100
3.06-3.250.25261380.20894561X-RAY DIFFRACTION100
3.25-3.50.24671460.19684559X-RAY DIFFRACTION100
3.5-3.860.22261350.18284609X-RAY DIFFRACTION100
3.86-4.410.19061390.1524655X-RAY DIFFRACTION100
4.41-5.560.16941450.15974679X-RAY DIFFRACTION100
5.56-49.140.18571510.17384927X-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://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