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- PDB-6qyf: 4'-phosphopantetheinyl transferase PptAb from Mycobacterium absce... -

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Basic information

Entry
Database: PDB / ID: 6qyf
Title4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus at pH 4.6 with Mg2+ and CoA.
ComponentsPossible 4'-phosphopantetheinyl transferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


enterobactin synthetase complex / enterobactin biosynthetic process / holo-[acyl-carrier-protein] synthase activity / magnesium ion binding / plasma membrane
Similarity search - Function
Enterobactin synthetase-like, component D / 4'-phosphopantetheinyl transferase, N-terminal domain / 4'-phosphopantetheinyl transferase N-terminal domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily
Similarity search - Domain/homology
COENZYME A / Possible 4'-phosphopantetheinyl transferase
Similarity search - Component
Biological speciesMycobacteroides abscessus ATCC 19977 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNguyen, M.C. / Mourey, L. / Pedelacq, J.D.
Funding support Netherlands, France, 2items
OrganizationGrant numberCountry
European Union (EU)10559 Netherlands
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
DepositionMar 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2243
Polymers25,4321
Non-polymers7922
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-14 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.080, 82.226, 55.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-886-

HOH

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Components

#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 / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1MD73
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Na acetate 30 % PEG 4K 0.2 M NH4 acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.4→28 Å / Num. obs: 56325 / % possible obs: 97 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 22.2
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 4954 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASERphasing
TRUNCATEdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U89

4u89


Resolution: 1.4→28 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.39
RfactorNum. reflection% reflection
Rfree0.1579 3018 2.81 %
Rwork0.1446 --
obs0.145 56311 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.87 Å2 / Biso mean: 22.2698 Å2 / Biso min: 8.88 Å2
Refinement stepCycle: final / Resolution: 1.4→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 81 488 2247
Biso mean--13.67 36.93 -
Num. residues----218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.36241150.28343993410883
1.42-1.450.29251280.25274381450990
1.45-1.470.18381390.21824716485596
1.47-1.50.23251340.20864772490698
1.5-1.530.22191400.18254840498099
1.53-1.560.19881410.17474846498799
1.56-1.590.18161370.16444845498299
1.59-1.630.15991430.14934815495899
1.63-1.670.18331410.14914797493899
1.67-1.710.17321430.14374929507299
1.71-1.760.19261380.14584826496499
1.76-1.820.14961390.142548735012100
1.82-1.890.16731450.140848715016100
1.89-1.960.16931410.145449195060100
1.96-2.050.13091420.13548585000100
2.05-2.160.13251410.130749085049100
2.16-2.290.13421380.12554843498199
2.29-2.470.12831330.13144611474494
2.47-2.720.18471350.13894734486997
2.72-3.110.17641430.13648795022100
3.11-3.920.13151380.13014813495198
3.92-280.13621240.14194382450689
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)
13.87962.23881.64164.6376-1.18042.17670.04670.1645-0.42750.0187-0.0237-0.26760.68220.1741-0.00260.15910.04-0.00420.12570.00110.149810.544896.1694129.99
21.9747-0.35810.09434.8726-0.9182.51520.00760.0120.2002-0.0069-0.0585-0.1707-0.15220.1880.05330.0710.0004-0.00680.099-0.01420.095710.545117.4055137.2083
34.564-2.0821-1.77363.80591.99675.2422-0.115-0.15040.01870.13040.1597-0.08230.04460.2158-0.02130.0712-0.0121-0.01070.06020.00780.090310.674111.3188134.4066
42.08110.0334-0.49961.06010.57671.9183-0.03710.07740.0606-0.07760.035-0.1133-0.05290.1430.00180.08310.00570.00140.09110.00760.10129.0967107.7232124.7903
53.44560.5748-1.83351.74520.65542.62530.07350.08250.055-0.0433-0.02190.0804-0.2297-0.292-0.00170.10340.00020.02750.12020.00020.0957-15.2066102.5093131.84
61.79810.3458-0.27451.2643-0.58552.1715-0.06140.2499-0.1002-0.08530.04640.00220.0898-0.08870.02210.0856-0.00310.00490.1216-0.0280.0851-6.938399.1045121.231
74.3634-0.406-3.9572.55540.4056.0588-0.03990.2449-0.1369-0.14020.0146-0.21810.17370.04560.06050.0906-0.00990.00150.0943-0.02650.13423.419997.1344123.5642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 21 )A5 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 42 )A22 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 62 )A43 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 114 )A63 - 114
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 128 )A115 - 128
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 208 )A129 - 208
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 222 )A209 - 222

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