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- PDB-5nji: Structure of the dehydratase domain of PpsC from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 5nji
TitleStructure of the dehydratase domain of PpsC from Mycobacterium tuberculosis in complex with C12:1-CoA
ComponentsPhthiocerol/phenolphthiocerol synthesis polyketide synthase type I PpsC
KeywordsTRANSFERASE / dehydratase / polyketide / complex / tuberculosis
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 / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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 / Phosphopantetheine attachment site. / Thiolase-like / 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
Chem-8Z2 / Phenolphthiocerol/phthiocerol polyketide synthase subunit C / Phenolphthiocerol/phthiocerol polyketide synthase subunit C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGavalda, S. / Faille, A. / Mourey, L. / Pedelacq, J.D.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Insights into Substrate Modification by Dehydratases from Type I Polyketide Synthases.
Authors: Faille, A. / Gavalda, S. / Slama, N. / Lherbet, C. / Maveyraud, L. / Guillet, V. / Laval, F. / Quemard, A. / Mourey, L. / Pedelacq, J.D.
History
DepositionMar 28, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionMay 31, 2017ID: 5CF7
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,2592
Polymers34,3111
Non-polymers9481
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.377, 70.810, 42.571
Angle α, β, γ (deg.)90.00, 104.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34311.336 Da / Num. of mol.: 1 / Mutation: H959F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ppsC, Rv2933 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7TXL8, UniProt: P96202*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-8Z2 / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (~{E})-dodec-2-enethioate


Mass: 947.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H56N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Na/K PO4 1.8 M / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97922 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.5→41.145 Å / Num. obs: 53493 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.9
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.71 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Coot0.8.6.1model building
PHENIX1.11.1-2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5iok

5iok


Resolution: 1.6→36.325 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 3197 3.71 %
Rwork0.1704 --
obs0.1713 44239 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→36.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 61 292 2339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232181
X-RAY DIFFRACTIONf_angle_d2.072995
X-RAY DIFFRACTIONf_dihedral_angle_d18.984894
X-RAY DIFFRACTIONf_chiral_restr0.103363
X-RAY DIFFRACTIONf_plane_restr0.01377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62390.28441400.2793622X-RAY DIFFRACTION99
1.6239-1.64930.27021400.2713639X-RAY DIFFRACTION99
1.6493-1.67630.28431410.2493602X-RAY DIFFRACTION99
1.6763-1.70520.26011380.22713645X-RAY DIFFRACTION99
1.7052-1.73620.26851350.21343563X-RAY DIFFRACTION99
1.7362-1.76960.20431440.21023718X-RAY DIFFRACTION99
1.7696-1.80570.22011380.19933595X-RAY DIFFRACTION99
1.8057-1.8450.19921440.20353650X-RAY DIFFRACTION99
1.845-1.88790.23181340.20583529X-RAY DIFFRACTION99
1.8879-1.93510.38181360.38053442X-RAY DIFFRACTION92
1.9351-1.98740.19591390.18343563X-RAY DIFFRACTION99
1.9874-2.04590.21021390.17123674X-RAY DIFFRACTION99
2.0459-2.11190.18261390.16373664X-RAY DIFFRACTION99
2.1119-2.18740.19081390.16163585X-RAY DIFFRACTION99
2.1874-2.2750.26241280.20563471X-RAY DIFFRACTION94
2.275-2.37850.17491410.15463653X-RAY DIFFRACTION99
2.3785-2.50390.20081390.15353603X-RAY DIFFRACTION99
2.5039-2.66070.15921420.15483643X-RAY DIFFRACTION99
2.6607-2.86610.21491440.16393632X-RAY DIFFRACTION99
2.8661-3.15430.16711400.16353596X-RAY DIFFRACTION99
3.1543-3.61040.16861410.15153641X-RAY DIFFRACTION99
3.6104-4.54740.14681340.12453588X-RAY DIFFRACTION98
4.5474-36.33420.16531420.15763644X-RAY DIFFRACTION99
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)
12.48860.86560.4740.82910.50760.9280.007-0.07330.0109-0.00080.0049-0.10580.04580.0814-0.02460.13020.00760.00520.10350.00310.144433.6198-3.768640.5268
23.1661.2351-0.17132.16220.25973.26420.0525-0.10750.31160.0786-0.04090.23160.0085-0.0202-0.08160.08530.0905-0.00350.0346-0.00220.182821.7774-2.131343.0296
34.7897-0.5278-0.02762.57430.28612.0877-0.0864-0.0932-0.06140.05630.02290.1160.1597-0.04030.06940.1576-0.03120.00720.09930.00140.133417.076-12.596842.1902
42.1907-0.69520.05332.8212-1.27153.21850.0896-0.04720.0903-0.0818-0.05080.25020.0565-0.1393-0.02910.1018-0.01030.00080.1105-0.02460.16713.8408-2.650244.4583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 926 through 1017 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1018 through 1081 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1082 through 1137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1138 through 1217 )

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