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- PDB-7ahb: Acyltransferase domain of the polyketide synthase PpsC of Mycobac... -

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Basic information

Entry
Database: PDB / ID: 7ahb
TitleAcyltransferase domain of the polyketide synthase PpsC of Mycobacterium tuberculosis
ComponentsPhthiocerol synthesis polyketide synthase type I PpsC
KeywordsTRANSFERASE / polyketide synthase / PpsC / acyltransferase / Mycobacterium turberculosis
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
Malonyl-CoA ACP transacylase, ACP-binding / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : ...Malonyl-CoA ACP transacylase, ACP-binding / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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 / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Phenolphthiocerol/phthiocerol polyketide synthase subunit C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFaille, A. / Mourey, L. / Pedelacq, J.D.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-09-BLAN-0298-01 France
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Molecular Basis for Extender Unit Specificity of Mycobacterial Polyketide Synthases.
Authors: Grabowska, A.D. / Brison, Y. / Maveyraud, L. / Gavalda, S. / Faille, A. / Nahoum, V. / Bon, C. / Guilhot, C. / Pedelacq, J.D. / Chalut, C. / Mourey, L.
History
DepositionSep 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,07531
Polymers75,5652
Non-polymers1,51029
Water9,782543
1
A: Phthiocerol synthesis polyketide synthase type I PpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,64317
Polymers37,7831
Non-polymers86116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
2
B: Phthiocerol synthesis polyketide synthase type I PpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,43114
Polymers37,7831
Non-polymers64913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
Unit cell
Length a, b, c (Å)51.374, 58.355, 65.857
Angle α, β, γ (deg.)65.839, 73.279, 71.019
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 37782.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ppsC, Rv2933 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P96202, (phenol)carboxyphthiodiolenone synthase

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Non-polymers , 5 types, 572 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 1.8 M ammonium sulfate, 0.2 M sodium thiocyanate, 0.1M Tris pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.9→48.12 Å / Num. obs: 49339 / % possible obs: 96.4 % / Redundancy: 2.1 % / Biso Wilson estimate: 20.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 4913 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
XDSdata reduction
Coot0.8.9.2model building
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QO3

2qo3


Resolution: 1.9→48.12 Å / SU ML: 0.2466 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.6561
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 3197 3.41 %
Rwork0.1878 90515 -
obs0.189 49328 91.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4863 0 79 543 5485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895039
X-RAY DIFFRACTIONf_angle_d0.80086836
X-RAY DIFFRACTIONf_chiral_restr0.0522783
X-RAY DIFFRACTIONf_plane_restr0.0063902
X-RAY DIFFRACTIONf_dihedral_angle_d20.30821799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.41561360.31243853X-RAY DIFFRACTION89.56
1.93-1.960.28981340.27893800X-RAY DIFFRACTION89.09
1.96-1.990.30381340.26063850X-RAY DIFFRACTION89.25
1.99-2.020.27461370.24383878X-RAY DIFFRACTION89.9
2.02-2.060.27131310.23913842X-RAY DIFFRACTION89.28
2.06-2.10.28881310.22693861X-RAY DIFFRACTION90.24
2.1-2.140.28761440.21773834X-RAY DIFFRACTION89.19
2.14-2.190.21871370.20433923X-RAY DIFFRACTION90.62
2.19-2.240.26351380.20153875X-RAY DIFFRACTION89.94
2.24-2.30.23911400.1993901X-RAY DIFFRACTION91.26
2.3-2.360.23471440.18563949X-RAY DIFFRACTION90.51
2.36-2.430.20111380.18473858X-RAY DIFFRACTION90.74
2.43-2.510.26851390.18693903X-RAY DIFFRACTION91.41
2.51-2.60.22761320.19523906X-RAY DIFFRACTION91.9
2.6-2.70.29391410.19744034X-RAY DIFFRACTION92.45
2.7-2.820.28541410.21283969X-RAY DIFFRACTION93.28
2.82-2.970.23561420.19793998X-RAY DIFFRACTION93.12
2.97-3.160.23241480.18984046X-RAY DIFFRACTION92.95
3.16-3.40.21831380.17853980X-RAY DIFFRACTION93.25
3.4-3.750.19751430.15824079X-RAY DIFFRACTION94.71
3.75-4.290.1671440.14044068X-RAY DIFFRACTION94.44
4.29-5.40.13861420.14854069X-RAY DIFFRACTION95.27
5.4-48.120.19171430.17374039X-RAY DIFFRACTION93.77
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)
13.181728773430.389034248696-0.3234995552092.14829687928-0.4354839612941.765327304110.603356744951-0.8691404610011.030505454331.02606437916-0.2435716077770.826658580013-0.790254636951-0.179314826131-0.3378490821210.57439021596-0.07597071542710.2143449587370.434529144236-0.1845573244320.5883565200760.4169346733688.8554608020720.5855399506
23.905302385542.17519368697-0.9558332095783.03814782716-1.48913595572.287300543980.138754705965-0.446544882854-0.09403675271450.199630705568-0.1067092662450.1941147987810.0927162885204-0.0686994721749-0.0739634457530.180340269065-0.02036915115030.007462220189250.2836544869740.06468057375220.226782478775-3.86082200116-10.377004477715.1603915565
32.71109087482-0.001095657007080.01734209905771.02336943057-0.2553186715020.7944922476560.140190727072-0.36495391529-0.1279309849640.0526989868059-0.0536385907622-0.06255082934190.02742568707690.0675576329061-0.07799064787430.142377937418-0.0419989600066-0.008033054818140.1991508314630.03969771263920.14186756285415.2225162572-12.442256263411.4342799898
41.982935934990.541172786950.02261012561442.681732755610.6902827983841.126005225670.117708977817-0.1188638476220.08994068772530.0211060080112-0.0703354038921-0.115819099182-0.08466566977320.0600435614518-0.07375279005150.139368832073-0.02773577750050.0110347473720.1804214748880.05193436284070.16563775928513.3327145073-4.156510357814.93354420792
53.8425796798-1.258949675511.58248348912.67119068555-1.32088170564.317678446280.4591329630730.77078507586-0.565300814117-0.697764790651-0.2094753206080.3615596810530.42513238144-0.147449020698-0.2404595990070.3155616215620.0783057420361-0.08880061420870.387995300846-0.05601516478930.323651869418-25.3406351073-1.29191477079-25.390477631
62.95407376056-0.8129294350111.016144832972.45360138176-0.8667216049542.759639253940.03579539734960.1967131583250.0307527064614-0.01148963178890.0647457801960.255473983896-0.0809374679529-0.167721642096-0.1030116899570.1084859534290.0007276628995470.005219207924950.2103940549050.0480199189630.171839854178-27.10420532358.68257209815-16.2464088564
73.65938320984-0.501058881057-1.268597111371.10945806579-0.08749823527811.455785686840.1661955340190.3433891710460.264891679846-0.0808063208922-0.0902119802227-0.137718675626-0.05768112316390.0542963568594-0.07915805748350.1305528871640.00313786887796-0.01701630363750.2055890559920.04447248558750.157910551002-7.0369030748415.5003292963-14.5475074031
82.66296909921-0.5352577902810.4225421161112.904787771111.07342630421.928386013290.2092559784950.303259669177-0.20757945919-0.147309924584-0.079585244968-0.1609264316470.1528930256070.0913176307088-0.1307343293130.1537144434160.0360973468509-0.02637950736160.2059770692290.05036038191240.19983280532-10.95750905580.589927793897-14.0713202455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 539 through 570 )A539 - 570
2X-RAY DIFFRACTION2chain 'A' and (resid 571 through 627 )A571 - 627
3X-RAY DIFFRACTION3chain 'A' and (resid 628 through 763 )A628 - 763
4X-RAY DIFFRACTION4chain 'A' and (resid 764 through 872 )A764 - 872
5X-RAY DIFFRACTION5chain 'B' and (resid 538 through 593 )B538 - 593
6X-RAY DIFFRACTION6chain 'B' and (resid 594 through 674 )B594 - 674
7X-RAY DIFFRACTION7chain 'B' and (resid 675 through 795 )B675 - 795
8X-RAY DIFFRACTION8chain 'B' and (resid 796 through 872 )B796 - 872

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