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

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Basic information

Entry
Database: PDB / ID: 6qxq
Title4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus at pH 7 with Mn2+ 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
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: 1.45 Å
AuthorsNguyen, M.C. / Mourey, L. / Pedelacq, J.D.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE18-0011-01 France
European Union (EU)10559 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 7, 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.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

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Assembly

Deposited unit
A: Possible 4'-phosphopantetheinyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3094
Polymers25,4321
Non-polymers8773
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-16 kcal/mol
Surface area10530 Å2
Unit cell
Length a, b, c (Å)62.941, 83.423, 56.130
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-743-

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 / Coenzyme A


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.9 Å3/Da / Density % sol: 57.54 % / Description: crystal
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES 23 % PEG 6K 0.1 M LiSO4

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 1.45→41.71 Å / Num. obs: 52990 / % possible obs: 99.73 % / Redundancy: 5.2 % / CC1/2: 0.998 / Net I/σ(I): 13.52
Reflection shellResolution: 1.45→1.502 Å / Num. unique obs: 5216 / CC1/2: 0.736

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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: 1.45→41.71 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.38
RfactorNum. reflection% reflection
Rfree0.1952 775 1.463 %
Rwork0.1667 --
obs0.1604 52955 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.47 Å2 / Biso mean: 30.21 Å2 / Biso min: 14.98 Å2
Refinement stepCycle: final / Resolution: 1.45→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 40 400 2115
Biso mean--21.7 42.49 -
Num. residues----218
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.49680.36081330.3161894099
1.4968-1.55030.27071300.27259017100
1.5503-1.61240.23571380.23119059100
1.6124-1.68580.24831350.21099063100
1.6858-1.77460.19191310.18869030100
1.7746-1.88580.19041340.1747895699
1.8858-2.03140.17861320.16549045100
2.0314-2.23590.19531350.15319089100
2.2359-2.55930.17591330.1486901399
2.5593-3.22430.20931370.1483899699
3.2243-41.710.16121360.13889027100
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)
13.76245.08063.33858.4794.36463.1525-0.0351-0.01750.7767-0.0719-0.15460.5207-0.5856-0.60710.23620.270.0601-0.00030.26790.01850.2979-9.897328.8294-11.6125
21.0765-0.2592-0.65974.4747-0.3383.4163-0.0215-0.0249-0.09240.26220.00670.1835-0.0496-0.12830.01220.12910.03220.0110.1824-0.00220.1832-11.933614.8601-0.9338
31.1332-0.18420.19871.4336-0.55191.7935-0.01780.1038-0.0835-0.05490.02560.14990.0674-0.1223-0.01710.16480.0041-0.00890.1802-0.02870.2063-9.327413.1044-12.0467
41.823-0.51173.40184.9659-2.94147.7286-0.0902-0.0974-0.09260.0039-0.0396-0.17580.61130.77560.12080.162-0.0259-0.02910.22060.00360.204615.571321.1051-7.9008
56.72251.5122-5.13823.42071.66348.6739-0.0884-0.03690.229-0.2190.119-0.2227-0.33850.565-0.05510.216-0.0312-0.04720.2780.00870.252816.636931.1832-11.5138
64.79183.67064.54664.07285.36237.7962-0.16260.18430.0624-0.1290.05890.0586-0.06530.14430.11490.18860.01150.00550.1810.02130.18425.211620.5359-16.4226
72.8686-1.1573-1.30259.32665.11065.68350.02130.31550.1735-0.09330.0212-0.2963-0.08040.1038-0.06380.1322-0.016-0.01030.20290.0440.13758.478624.5799-20.3998
82.7217-0.17550.32591.69910.15545.45930.16910.60650.0438-0.3873-0.041-0.0242-0.3541-0.4762-0.06680.1589-0.0156-0.01820.28110.03080.2132.268623.9858-24.2643
97.2112-0.61865.11533.8159-0.75573.99150.04650.41450.2004-0.2574-0.0790.2674-0.02770.01930.06720.1516-0.0069-0.0120.15420.0330.2163-3.045326.498-16.5936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 17 )A5 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 31 )A18 - 31
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 114 )A32 - 114
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 128 )A115 - 128
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 143 )A129 - 143
6X-RAY DIFFRACTION6chain 'A' and (resid 144 through 163 )A144 - 163
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 186 )A164 - 186
8X-RAY DIFFRACTION8chain 'A' and (resid 187 through 208 )A187 - 208
9X-RAY DIFFRACTION9chain 'A' and (resid 209 through 222 )A209 - 222

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