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- PDB-6d8i: Mycobacterium tuberculosis polyketide synthase 13 N-terminal acyl... -

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Basic information

Entry
Database: PDB / ID: 6d8i
TitleMycobacterium tuberculosis polyketide synthase 13 N-terminal acyl carrier protein domain
ComponentsPolyketide synthase
KeywordsBIOSYNTHETIC PROTEIN / PKS13 / N-terminal ACP
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 domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase ...Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / : / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsTang, S. / Sacchettini, J.
CitationJournal: To be Published
Title: Mycobacterium tuberculosis polyketide synthase 13 N-terminal acyl carrier protein domain
Authors: Tang, S. / Sacchettini, J.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9958
Polymers9,5381
Non-polymers4577
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-17 kcal/mol
Surface area4890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.646, 51.646, 75.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Polyketide synthase /


Mass: 9538.201 Da / Num. of mol.: 1
Fragment: N-terminal acyl carrier protein domain (UNP residues 10-93)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: LH57_20715 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A089QYU6, UniProt: I6X8D2*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate, 18-24% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2014
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 12903 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 15.68 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.036 / Rrim(I) all: 0.138 / Χ2: 1.445 / Net I/σ(I): 5.4 / Num. measured all: 181018
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.65-1.6814.10.7256260.8940.1980.7510.419
1.68-1.7114.30.576310.9440.1550.5910.427
1.71-1.7414.20.5316270.9410.1450.5510.432
1.74-1.7814.30.4936320.9540.1340.5120.465
1.78-1.8214.30.4476170.9640.1210.4630.472
1.82-1.8614.20.346330.9790.0920.3520.501
1.86-1.914.30.3096310.9780.0840.320.535
1.9-1.9614.30.2536220.9840.0690.2630.653
1.96-2.0114.30.236360.9890.0620.2380.762
2.01-2.0814.20.2126400.9920.0580.220.895
2.08-2.1514.20.1726530.9920.0470.1781.01
2.15-2.2414.30.1646240.9910.0440.171.126
2.24-2.3414.20.1446500.9950.0390.151.203
2.34-2.4614.10.1346470.9950.0360.1391.389
2.46-2.6214.10.136340.9950.0350.1341.75
2.62-2.8214.10.1376520.9950.0370.1422.36
2.82-3.1113.90.1156490.9950.0320.122.608
3.11-3.5513.80.0976630.9970.0270.1013.098
3.55-4.4813.40.0856790.9980.0240.0883.835
4.48-5012.20.0927570.9980.0260.0964.87

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13rc1_2954refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→42.556 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.57 / Phase error: 15.39
RfactorNum. reflection% reflection
Rfree0.1797 1286 10 %
Rwork0.1641 --
obs0.1657 12855 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.68 Å2 / Biso mean: 20.2094 Å2 / Biso min: 8.43 Å2
Refinement stepCycle: final / Resolution: 1.65→42.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms596 0 57 91 744
Biso mean--41.94 29.65 -
Num. residues----79
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.648-1.7140.23891390.195612501389
1.714-1.7920.20891400.180912611401
1.792-1.88650.20051380.162812421380
1.8865-2.00470.16681410.150512671408
2.0047-2.15950.16811420.148612731415
2.1595-2.37680.18181410.142112761417
2.3768-2.72060.16471440.158512921436
2.7206-3.42750.17721450.159813051450
3.4275-42.57040.17771560.179214031559
Refinement TLS params.Method: refined / Origin x: 29.1925 Å / Origin y: 8.5159 Å / Origin z: 25.3785 Å
111213212223313233
T0.1184 Å20.0007 Å20.0091 Å2-0.1212 Å2-0.0011 Å2--0.099 Å2
L1.8673 °20.2092 °20.4412 °2-1.4608 °2-0.4451 °2--1.5709 °2
S0.0434 Å °-0.1395 Å °0.0066 Å °0.1155 Å °-0.0184 Å °0.0748 Å °-0.0658 Å °-0.0801 Å °-0.0296 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA15 - 93
2X-RAY DIFFRACTION1allS1 - 91
3X-RAY DIFFRACTION1allB1 - 3
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1 - 3

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