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- PDB-9c1c: Mycobacterium tuberculosis PKS13 acyltransferase serine converted... -

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Basic information

Entry
Database: PDB / ID: 9c1c
TitleMycobacterium tuberculosis PKS13 acyltransferase serine converted to beta-lactam form by CEC215 via SuFEx reaction
Components(Polyketide synthase ...) x 2
KeywordsANTIBIOTIC / inhibitor / 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 H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,96052
Polymers159,2053
Non-polymers3,75449
Water5,693316
1
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,40031
Polymers53,0561
Non-polymers2,34530
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-245 kcal/mol
Surface area20130 Å2
MethodPISA
2
B: Polyketide synthase Pks13
D: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,55921
Polymers106,1502
Non-polymers1,41019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-114 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.524, 106.524, 258.644
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-1106-

SO4

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Components

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Polyketide synthase ... , 2 types, 3 molecules ABD

#1: Protein Polyketide synthase Pks13


Mass: 53055.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pks13, Rv3800c / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein Polyketide synthase Pks13


Mass: 53074.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pks13, Rv3800c / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 8 types, 365 molecules

#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsThe authors state that the recombinant protein contains His-TEV cleavable tag. Residues SNA at the ...The authors state that the recombinant protein contains His-TEV cleavable tag. Residues SNA at the N-terminus was from the pMCSG7 vector backbone after TEV cleavage. Residue serine 229 (801 in the original protein numbering) was converted to beta-lactam through reacting with small molecule inhibitor CEC215.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.62 %
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

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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: Apr 6, 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: 83855 / % possible obs: 89.1 % / Redundancy: 9.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.045 / Rrim(I) all: 0.151 / Χ2: 0.509 / Net I/σ(I): 3.4 / Num. measured all: 803445
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.12-2.162.11.78926050.2440.6261.222.1830.4256.4
2.16-2.212.72.06734210.1850.5581.2192.4210.41773.9
2.21-2.263.81.95440070.2550.6380.9262.1780.45986.2
2.26-2.315.51.87643430.4660.7970.7342.0240.43893.6
2.31-2.377.11.71144940.5450.840.6061.8220.43196.8
2.37-2.439.41.50546280.6760.8980.4681.580.42898.9
2.43-2.510.51.22645870.7810.9360.3731.2830.43699.5
2.5-2.5811.40.97246540.8410.9560.2851.0150.44199.7
2.58-2.6811.60.7846720.9030.9740.2280.8140.44599.7
2.68-2.7811.40.58646730.9390.9840.1730.6120.45299.9
2.78-2.9111.10.4146860.9610.990.1240.4290.45799.9
2.91-3.0611.50.29546870.9810.9950.0880.3080.483100
3.06-3.2511.80.247290.990.9980.0590.2090.509100
3.25-3.5112.10.13447280.9950.9990.0390.140.541100
3.51-3.8611.90.09647500.9970.9990.0290.10.598100
3.86-4.4212.40.06648020.99810.0190.0690.624100
4.42-5.5612.60.05748420.99910.0160.0590.638100
5.56-5012.20.04151430.99910.0120.0420.587100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→49.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.711 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23516 2770 3.8 %RANDOM
Rwork0.19055 ---
obs0.19219 70609 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.584 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.54 Å2
Refinement stepCycle: 1 / Resolution: 2.22→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7159 0 194 316 7669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166976
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.81810123
X-RAY DIFFRACTIONr_angle_other_deg0.5641.73416046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.681549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.892101144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021622
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8374.7343779
X-RAY DIFFRACTIONr_mcbond_other3.8354.7343779
X-RAY DIFFRACTIONr_mcangle_it5.5858.4914717
X-RAY DIFFRACTIONr_mcangle_other5.5868.4934718
X-RAY DIFFRACTIONr_scbond_it5.1675.323677
X-RAY DIFFRACTIONr_scbond_other55.2773582
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3959.4435261
X-RAY DIFFRACTIONr_long_range_B_refined8.89146.18128
X-RAY DIFFRACTIONr_long_range_B_other8.88745.768084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 181 -
Rwork0.352 4623 -
obs--89.31 %

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