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- PDB-4ooc: Dehydratase domain of the polyketide PpsC from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 4ooc
TitleDehydratase domain of the polyketide PpsC from Mycobacterium tuberculosis
ComponentsPhthiocerol synthesis polyketide synthase type I PpsC
KeywordsTRANSFERASE / dehydratase
Function / homology
Function and homology information


(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process ...(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyketide synthase dehydratase / Zinc-binding dehydrogenase / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...Polyketide synthase dehydratase / Zinc-binding dehydrogenase / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Thiol Ester Dehydrase; Chain A / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / 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 / GroES-like superfamily / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phenolphthiocerol/phthiocerol polyketide synthase subunit C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsFaille, A. / Mourey, L. / Pedelacq, J.D.
CitationJournal: To be Published
Title: Insights into the catalytic mechanism of the DH domain of the Mycobacterium tuberculosis polyketide synthase PpsC and architecture of the beta-carbon processing domains
Authors: Faille, A. / Slama, N. / Quemard, A. / Mourey, L. / Pedelacq, J.D.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phthiocerol synthesis polyketide synthase type I PpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5542
Polymers34,4591
Non-polymers951
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.506, 89.506, 159.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phthiocerol synthesis polyketide synthase type I PpsC / Beta-ketoacyl-acyl-carrier-protein synthase I


Mass: 34459.438 Da / Num. of mol.: 1 / Fragment: dehydratase domain (UNP residues 921-1222)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ppsC, Rv2933 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96202, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.6373.43
24.6373.43
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop6.31.8 M sodium/potassium phosphate pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop616% PEG8000, 20% glycerol, 0.04 M potassium phosphate monobasic, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.97914, 0.97930
SYNCHROTRONESRF ID14-420.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 9, 2009
ADSC QUANTUM 315r2CCDMar 7, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979141
20.97931
30.97951
ReflectionNumber: 286453 / Rmerge(I) obs: 0.105 / Χ2: 1.56 / D res high: 3 Å / Num. obs: 24832 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.8636.38195298.310.038
6.328.86169110010.05
5.186.32220510010.069
4.495.18256610010.07
4.024.49292310010.094
3.674.02323110010.18
3.43.67350410010.298
3.183.4376299.910.73
33.18399899.611.54
ReflectionResolution: 2.62→36.381 Å / Num. obs: 19876 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.52
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.62-2.770.9581.291,288.4
2.77-2.960.7432.391,2100
2.96-3.20.364.661,2100
3.2-3.50.1579.181,2100
3.5-3.910.0915.91,2100
3.91-4.510.05426.81,299.9
4.51-5.50.04134.561,2100
5.5-7.710.03440.191,299.9
7.710.02152.051,295.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→36.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.2488 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25062 935 5.1 %RANDOM
Rwork0.20777 ---
obs0.2099 17486 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 5 5 1988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192015
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.9632759
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.625265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53423.90282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.74115300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4571516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211518
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 66 -
Rwork0.48 1259 -
obs--99.7 %

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