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

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Basic information

Entry
Database: PDB / ID: 6qyg
Title4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus at pH 8.5 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 speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / 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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2484
Polymers25,4321
Non-polymers8163
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-24 kcal/mol
Surface area10590 Å2
Unit cell
Length a, b, c (Å)55.422, 60.334, 66.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Gene: MAB_3117c / 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS 30 % PEG 4K 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 1.6→42.46 Å / Num. obs: 29270 / % possible obs: 98 % / Redundancy: 5.5 % / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 2856 / CC1/2: 0.797

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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: 1.6→42.46 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36
RfactorNum. reflection% reflection
Rfree0.1956 2479 4.51 %
Rwork0.1809 --
obs0.1807 29268 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.96 Å2 / Biso mean: 25.3524 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 1.6→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 42 314 2039
Biso mean--20.89 33.21 -
Num. residues----219
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.63080.31261310.2804290097
1.6308-1.66410.26651420.282286797
1.6641-1.70030.2851270.2737296997
1.7003-1.73980.22711220.2682289697
1.7398-1.78340.27081500.262286895
1.7834-1.83160.24761390.2314293498
1.8316-1.88550.24071340.2206292298
1.8855-1.94630.21911370.2065298198
1.9463-2.01590.16231510.1868289099
2.0159-2.09660.22961350.1771294198
2.0966-2.1920.22441390.1804287796
2.192-2.30760.22421360.1766296199
2.3076-2.45220.21781370.1738296199
2.4522-2.64150.18051420.1786299599
2.6415-2.90720.16151330.17286796
2.9072-3.32780.16771450.15562970100
3.3278-4.19220.14531430.1457292898
4.1922-42.460.19051360.1618293798
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)
12.9914-1.0261.70976.7331-1.28154.70640.0429-0.150.57750.1332-0.0801-0.3762-0.45090.26230.03110.1919-0.05010.00570.1709-0.02120.1958-24.26128.17634.1717
23.1638-1.5478-1.03522.90891.10352.7276-0.0646-0.0313-0.14620.09860.0585-0.16920.24470.22170.01940.1390.0146-0.01520.15570.00220.1443-20.05-10.15836.4136
31.47030.1096-0.90271.1267-0.62542.9804-0.0213-0.0144-0.0472-0.0451-0.0243-0.08230.08220.05270.04780.12960.007-0.00740.1135-0.00630.1505-27.9903-2.6288-1.4603
44.54882.3737-1.87241.743-1.24581.4384-0.05710.40820.1414-0.17750.11970.00350.0689-0.0752-0.050.17020.02130.0130.16560.02640.1599-29.2752.6255-15.4344
58.42552.91390.52041.95430.65830.81930.05660.10450.3772-0.02050.01430.0641-0.1148-0.1003-0.05270.16340.03050.02450.14310.05010.1658-35.66866.781-10.1688
65.7024-1.1328-0.04022.51410.00822.7722-0.0356-0.22920.02070.29230.00580.2193-0.1864-0.14860.04110.212600.03380.11570.02510.1982-31.29177.1892-2.898
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 62 )A22 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 128 )A63 - 128
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 176 )A129 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 208 )A177 - 208
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 223 )A209 - 223

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