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- PDB-6rcx: Mycobacterial 4'-phosphopantetheinyl transferase PptAb in complex... -

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Basic information

Entry
Database: PDB / ID: 6rcx
TitleMycobacterial 4'-phosphopantetheinyl transferase PptAb in complex with the ACP domain of PpsC.
Components
  • Phthiocerol synthesis polyketide synthase type I PpsC
  • Possible 4'-phosphopantetheinyl transferase
KeywordsTRANSFERASE/TRANSPORT PROTEIN / TRANSFERASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / enterobactin synthetase complex / Actinobacterium-type cell wall biogenesis / enterobactin biosynthetic process / DIM/DIP cell wall layer assembly / holo-[acyl-carrier-protein] synthase activity / fatty acid synthase activity ...(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / enterobactin synthetase complex / Actinobacterium-type cell wall biogenesis / enterobactin biosynthetic process / DIM/DIP cell wall layer assembly / holo-[acyl-carrier-protein] synthase activity / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / magnesium ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Enterobactin synthetase-like, component D / 4'-phosphopantetheinyl transferase, N-terminal domain / 4'-phosphopantetheinyl transferase N-terminal domain / Zinc-binding dehydrogenase / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / : ...Enterobactin synthetase-like, component D / 4'-phosphopantetheinyl transferase, N-terminal domain / 4'-phosphopantetheinyl transferase N-terminal domain / Zinc-binding dehydrogenase / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / : / 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 / 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
Similarity search - Domain/homology
CACODYLATE ION / COENZYME A / : / Possible 4'-phosphopantetheinyl transferase / Phenolphthiocerol/phthiocerol polyketide synthase subunit C
Similarity search - Component
Biological speciesMycobacteroides abscessus ATCC 19977 (bacteria)
Mycobacterium abscessus ATCC 19977 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNguyen, M.C. / Mourey, L. / Pedelacq, J.D.
Funding support France, 2items
OrganizationGrant numberCountry
European Union (EU)10559 France
French National Research AgencyANR-16-CE18-0011-01 France
CitationJournal: Febs J. / Year: 2020
Title: Conformational flexibility of coenzyme A and its impact on the post-translational modification of acyl carrier proteins by 4'-phosphopantetheinyl transferases.
Authors: Nguyen, M.C. / Saurel, O. / Carivenc, C. / Gavalda, S. / Saitta, S. / Tran, M.P. / Milon, A. / Chalut, C. / Guilhot, C. / Mourey, L. / Pedelacq, J.D.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Jan 24, 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: Possible 4'-phosphopantetheinyl transferase
B: Phthiocerol synthesis polyketide synthase type I PpsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2937
Polymers42,2242
Non-polymers1,0695
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-27 kcal/mol
Surface area13070 Å2
Unit cell
Length a, b, c (Å)50.142, 63.167, 108.459
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Possible 4'-phosphopantetheinyl transferase


Mass: 25432.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus ATCC 19977 (bacteria)
Gene: MAB_3117c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1MD73
#2: Protein Phthiocerol synthesis polyketide synthase type I PpsC / Beta-ketoacyl-acyl-carrier-protein synthase I


Mass: 16791.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACP fragment from position 2056 to 2188 mutation S2105A
Source: (gene. exp.) Mycobacterium abscessus ATCC 19977 (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ppsC, Rv2933 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P96202, beta-ketoacyl-[acyl-carrier-protein] synthase I

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Non-polymers , 4 types, 149 molecules

#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6AsO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Na Cacodylate 30 % PEG 8K 0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→41.15 Å / Num. obs: 23870 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.998 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 12069 / CC1/2: 0.929

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHASERphasing
TRUNCATEdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u89

4u89


Resolution: 2→41.15 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.96
RfactorNum. reflection% reflection
Rfree0.2436 3214 7.21 %
Rwork0.2058 --
obs0.2084 23853 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.45 Å2 / Biso mean: 50.3859 Å2 / Biso min: 22.19 Å2
Refinement stepCycle: final / Resolution: 2→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 56 144 2439
Biso mean--51.78 47.57 -
Num. residues----292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.02990.34291380.3157175598
2.0299-2.06160.31821420.3098182199
2.0616-2.09540.32081420.28511780100
2.0954-2.13160.33091370.2745181699
2.1316-2.17030.31611450.2841181899
2.1703-2.21210.32131370.2881175399
2.2121-2.25720.2661380.293182399
2.2572-2.30630.36981390.2835180499
2.3063-2.360.36631390.2915181199
2.36-2.4190.33941390.2884178199
2.419-2.48440.34111400.2932179099
2.4844-2.55750.31861400.2627178099
2.5575-2.640.32311410.2421182499
2.64-2.73440.29471350.2281781100
2.7344-2.84380.28241350.23321826100
2.8438-2.97320.24261380.21811811100
2.9732-3.12990.22391410.2077181199
3.1299-3.3260.28231370.2064180599
3.326-3.58270.21141360.17841820100
3.5827-3.94310.1951440.16181781100
3.9431-4.51320.19531470.14571819100
4.5132-5.68440.19411390.1513179199
5.6844-41.150.18931450.1757178599
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)
17.54715.163-5.55513.5329-3.80084.0895-0.0122.59211.4986-2.45650.12060.1441-2.2422-1.3125-0.15161.16650.0109-0.01640.76740.15990.4516-9.542823.3365-30.1903
21.51410.3401-0.07663.0265-0.24382.38730.1174-0.11160.22680.3-0.1590.0463-0.4015-0.00150.01660.3338-0.00980.01150.2655-0.0010.2706-3.855722.4481-16.272
33.4493-0.1214-0.76153.30290.13576.29020.0833-0.0675-0.070.0837-0.08980.2950.0715-0.43080.03880.1429-0.00780.00360.2506-0.00690.2819-16.21527.8174-18.4449
41.43623.21440.30868.9809-3.4579.85340.7241-0.1116-0.5380.3904-0.3977-0.84111.18331.7249-0.29520.54210.0695-0.10840.5872-0.12130.583812.92030.5866-9.0365
59.0519-1.20045.64067.515-2.66767.68770.3354-0.0062-0.13270.21290.0424-0.05850.5097-0.1394-0.32930.4392-0.0338-0.00850.3146-0.00030.23834.3053.9474-10.553
65.27265.7983-0.42819.51910.51660.34641.1015-0.1323-0.70070.2922-0.06250.79871.3051-1.3323-0.96210.9328-0.1869-0.28840.73050.16240.68021.6714-1.059-3.7377
76.69794.09415.29525.35383.31575.44960.74780.5448-0.68410.75170.06070.3017-0.5855-0.4965-0.60161.5767-0.5608-0.09350.98680.23891.01621.9995-7.46682.9083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 8 )A4 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 123 )A9 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 220 )A124 - 220
4X-RAY DIFFRACTION4chain 'B' and (resid 30 through 52 )B30 - 52
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 75 )B53 - 75
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 100 )B76 - 100
7X-RAY DIFFRACTION7chain 'B' and (resid 101 through 104 )B101 - 104

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