[English] 日本語
Yorodumi
- PDB-6p9k: Crystal structure of Mycobacterium tuberculosis KasA in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p9k
TitleCrystal structure of Mycobacterium tuberculosis KasA in complex with O6G
Components3-oxoacyl-ACP synthase
KeywordsTRANSFERASE / BETA KETOACYL SYNTHASE I / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase I / fatty acid elongation, saturated fatty acid / beta-ketoacyl-[acyl-carrier-protein] synthase I / fatty acid elongation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-O6G / 3-oxoacyl-ACP synthase / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsCapodagli, G.C. / Neiditch, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109713 United States
CitationJournal: Cell Chem Biol / Year: 2020
Title: A Preclinical Candidate Targeting Mycobacterium tuberculosis KasA.
Authors: Inoyama, D. / Awasthi, D. / Capodagli, G.C. / Tsotetsi, K. / Sukheja, P. / Zimmerman, M. / Li, S.G. / Jadhav, R. / Russo, R. / Wang, X. / Grady, C. / Richmann, T. / Shrestha, R. / Li, L. / ...Authors: Inoyama, D. / Awasthi, D. / Capodagli, G.C. / Tsotetsi, K. / Sukheja, P. / Zimmerman, M. / Li, S.G. / Jadhav, R. / Russo, R. / Wang, X. / Grady, C. / Richmann, T. / Shrestha, R. / Li, L. / Ahn, Y.M. / Ho Liang, H.P. / Mina, M. / Park, S. / Perlin, D.S. / Connell, N. / Dartois, V. / Alland, D. / Neiditch, M.B. / Kumar, P. / Freundlich, J.S.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
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: 3-oxoacyl-ACP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8499
Polymers43,1421
Non-polymers7078
Water5,170287
1
A: 3-oxoacyl-ACP synthase
hetero molecules

A: 3-oxoacyl-ACP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,69718
Polymers86,2832
Non-polymers1,41416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8240 Å2
ΔGint-36 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.505, 77.505, 145.167
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

21A-747-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein 3-oxoacyl-ACP synthase


Mass: 43141.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: kasA_2, kasA, kasA_1, ERS007663_00367, ERS007672_01613, ERS007679_01974, ERS007681_02066, ERS007688_01478, ERS007703_02203, ERS007722_03184, ERS007741_02349, ERS023446_01403, ERS024276_01522, ...Gene: kasA_2, kasA, kasA_1, ERS007663_00367, ERS007672_01613, ERS007679_01974, ERS007681_02066, ERS007688_01478, ERS007703_02203, ERS007722_03184, ERS007741_02349, ERS023446_01403, ERS024276_01522, ERS027644_00736, ERS027646_00897, ERS027651_00106, ERS027652_01351, ERS027656_00221, ERS027659_01260, ERS027666_02494, ERS031537_00603, ERS124361_03146, SAMEA2683035_01249
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0A045JQD6, UniProt: P9WQD9*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I

-
Non-polymers , 5 types, 295 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-O6G / N-(2-cyano-3-methyl-1H-indol-5-yl)butane-1-sulfonamide


Mass: 291.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 200mM NaCl, 6% Isopropanol, 1mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP HCl)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 56051 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.022 / Rrim(I) all: 0.068 / Χ2: 0.934 / Net I/av σ(I): 20.2 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7310.20.54627640.9080.1790.5750.488100
1.73-1.7610.20.43827550.9440.1430.4610.453100
1.76-1.79100.37127730.9590.1230.3910.47100
1.79-1.83100.327540.9710.0990.3160.493100
1.83-1.879.80.26627630.9760.0890.2810.506100
1.87-1.919.70.26327950.9780.0890.2780.67499.9
1.91-1.968.80.20727460.9840.0730.220.622100
1.96-2.029.70.15827620.990.0530.1670.651100
2.02-2.0710.30.15327960.9920.050.1610.817100
2.07-2.1410.30.12527800.9930.0410.1310.776100
2.14-2.2210.10.11228090.9940.0370.1180.848100
2.22-2.3110.10.10727550.9950.0350.1131.028100
2.31-2.41100.09228110.9950.030.0971.018100
2.41-2.5490.08327670.9960.0290.0891.11499.9
2.54-2.710.20.0828140.9960.0260.0841.227100
2.7-2.9110.40.07128210.9970.0230.0751.281100
2.91-3.210.20.06528300.9980.0210.0691.398100
3.2-3.669.30.05828390.9980.020.0611.604100
3.66-4.619.90.05328820.9980.0170.0561.765100
4.61-509.30.04630350.9990.0160.0491.37499.8

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W2O

5w2o


Resolution: 1.703→39.252 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.83
RfactorNum. reflection% reflection
Rfree0.1693 1993 3.56 %
Rwork0.1443 --
obs0.1451 55990 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.99 Å2 / Biso mean: 35.5983 Å2 / Biso min: 17.67 Å2
Refinement stepCycle: final / Resolution: 1.703→39.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 47 287 3358
Biso mean--45.34 43.77 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7027-1.74530.19921380.16413783392199
1.7453-1.79250.16581380.153938273965100
1.7925-1.84520.17631430.14638103953100
1.8452-1.90480.17931420.15137803922100
1.9048-1.97290.18061420.150238333975100
1.9729-2.05190.15511420.140538083950100
2.0519-2.14520.18011420.143138413983100
2.1452-2.25830.16151440.140838293973100
2.2583-2.39980.21291380.153338333971100
2.3998-2.58510.18461420.150538694011100
2.5851-2.84510.17491390.156838503989100
2.8451-3.25670.18821450.153139114056100
3.2567-4.10240.1651460.134939354081100
4.1024-39.26260.1451520.136940884240100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.28080.0563-0.57552.1560.43161.36510.1803-0.05170.25270.1269-0.1549-0.0582-0.2478-0.0443-0.04190.3356-0.0448-0.02470.1590.01570.2285-36.200716.47-11.0488
21.92850.6288-0.59252.8042-0.30724.40820.16080.23090.1501-0.1782-0.21770.3996-0.4837-0.39960.04530.35880.077-0.00370.2801-0.03730.3135-50.233716.9087-20.1026
32.41-0.082-0.90740.87060.2531.38530.26080.14910.2174-0.2519-0.1997-0.2344-0.4217-0.0014-0.06380.39170.02390.05490.17570.05540.2512-33.445116.3594-26.84
43.30831.02521.69081.3971.42282.9615-0.0031-0.11970.17390.003-0.23070.5914-0.0427-0.48920.24660.37360.07350.02170.3115-0.0710.4502-54.6684.4954-33.1647
50.9315-0.18810.04261.76360.36191.06960.1746-0.09590.04580.1789-0.1417-0.1948-0.03420.0245-0.03060.2859-0.0601-0.0310.14940.02990.2237-32.78816.7405-13.8464
60.9805-0.1014-0.01171.71240.66541.21440.1712-0.2397-0.00950.5028-0.1011-0.31780.04990.0728-0.06080.4298-0.126-0.09590.22180.02630.2813-28.16639.4993-2.1916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 54 )A3 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 81 )A55 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 118 )A82 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 146 )A119 - 146
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 298 )A147 - 298
6X-RAY DIFFRACTION6chain 'A' and (resid 299 through 416 )A299 - 416

+
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