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

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Basic information

Entry
Database: PDB / ID: 6qxr
Title4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus at pH 8.5 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 speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 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 / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,3505
Polymers25,4321
Non-polymers9174
Water7,296405
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-26 kcal/mol
Surface area10680 Å2
Unit cell
Length a, b, c (Å)55.361, 60.589, 66.365
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 / 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: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS 25 % PEG 4K 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 1.2→44.75 Å / Num. obs: 68697 / % possible obs: 97.6 % / Redundancy: 3.2 % / CC1/2: 0.999 / Net I/σ(I): 13.1
Reflection shellResolution: 1.2→44.75 Å / Num. unique obs: 6755 / CC1/2: 0.724

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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: 1.2→44.75 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.95
RfactorNum. reflection% reflection
Rfree0.1785 2959 2.36 %
Rwork0.16 --
obs0.1604 68693 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.44 Å2 / Biso mean: 20.5055 Å2 / Biso min: 7.77 Å2
Refinement stepCycle: final / Resolution: 1.2→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 40 405 2133
Biso mean--12.21 30.86 -
Num. residues----220
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21970.29571440.2904577793
1.2197-1.24070.3021390.2776586793
1.2407-1.26330.27371500.2681585493
1.2633-1.28760.26461380.2556569191
1.2876-1.31390.24541390.2445581093
1.3139-1.34240.27851510.234602396
1.3424-1.37370.27061420.2251598796
1.3737-1.4080.22711480.2077596695
1.408-1.44610.21371370.2042588594
1.4461-1.48860.20471350.1904570191
1.4886-1.53670.18761480.1715607397
1.5367-1.59160.18341480.1619606297
1.5916-1.65530.17011430.1587598495
1.6553-1.73070.20881420.1622591494
1.7307-1.82190.1521420.1591558990
1.8219-1.93610.14691350.1532596995
1.9361-2.08560.18381470.1438594694
2.0856-2.29540.15181400.1389577992
2.2954-2.62760.16291260.139547887
2.6276-3.31030.14061310.1366579792
3.3103-44.750.16581340.1323544887
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)
16.91490.12581.11587.32531.72767.3991-0.006-0.1570.6339-0.148-0.07640.2292-0.5735-0.10560.00040.14420.0256-0.00830.09440.0090.152452.568369.3238-4.153
21.92331.48221.79252.10132.77853.7188-0.0395-0.20750.115-0.0649-0.020.31670.1455-0.1170.02410.1184-0.0186-0.01230.17890.00980.158840.862855.2644-7.2656
34.06671.7792-1.77324.3904-2.00965.121-0.09720.0073-0.4672-0.0796-0.1335-0.04840.2811-0.08720.06180.1699-0.01010.00810.1314-0.00810.178751.179342.6758-6.5343
46.59625.1488-4.98187.4126-6.25998.6783-0.0771-0.0255-0.27040.00670.05250.09680.2793-0.2838-0.01860.1017-0.0221-0.00330.1232-0.01620.094546.6850.6804-3.5043
53.4181-0.42180.98066.0336-3.76565.79680.01150.1376-0.0242-0.25750.08130.08140.2082-0.1271-0.1120.1025-0.0090.00220.0994-0.00020.068656.318355.8442-12.3114
60.75330.2218-0.54321.00390.49852.71130.00450.01720.01290.0147-0.05410.00990.021-0.03540.04230.0809-0.0002-0.00490.07160.00890.078156.002658.90640.3679
79.27971.03432.36293.61141.5424.17510.1245-0.4959-0.48560.2819-0.09740.08230.3712-0.0988-0.07160.1768-0.01870.03690.14-0.00180.127852.489259.967523.4962
83.0806-1.614-1.65541.45341.29021.8235-0.0419-0.15790.0470.11720.00810.04280.01640.02190.06240.0862-0.01480.00630.0719-0.01660.079256.678862.503214.8718
96.2446-2.6366-0.20472.3187-0.26341.6012-0.0929-0.17520.16860.10070.0988-0.0027-0.0930.079-0.01650.1047-0.02720.00250.0825-0.0310.10664.235966.575513.4111
109.6954-1.36860.2691.3922-0.03331.10650.10590.28950.3359-0.0478-0.07890.0665-0.0771-0.0010.0040.12140.00060.01090.0908-0.00850.100956.506668.10977.1393
117.36223.9374-3.9693.4885-1.68034.4148-0.0631-0.26630.0228-0.1911-0.0258-0.7082-0.27170.74920.09150.1501-0.05860.04820.2237-0.01490.296969.684168.82840.8972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 20 )A5 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 29 )A21 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 41 )A30 - 41
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 56 )A42 - 56
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 72 )A57 - 72
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 118 )A73 - 118
7X-RAY DIFFRACTION7chain 'A' and (resid 119 through 130 )A119 - 130
8X-RAY DIFFRACTION8chain 'A' and (resid 131 through 171 )A131 - 171
9X-RAY DIFFRACTION9chain 'A' and (resid 172 through 194 )A172 - 194
10X-RAY DIFFRACTION10chain 'A' and (resid 195 through 214 )A195 - 214
11X-RAY DIFFRACTION11chain 'A' and (resid 215 through 224 )A215 - 224

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