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

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Basic information

Entry
Database: PDB / ID: 6qwu
Title4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus at pH 5.5 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 / : / DI(HYDROXYETHYL)ETHER / 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 France, 1items
OrganizationGrant numberCountry
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 6, 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)26,4396
Polymers25,4321
Non-polymers1,0075
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-19 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.652, 61.918, 66.699
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 335 molecules

#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.26 Å3/Da / Density % sol: 45.56 % / Description: crystal
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 5.5 / Details: 0.1 M Bis-Tris 25 % PEG3350 0.2 M NaCl

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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 PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.4→45.38 Å / Num. obs: 45439 / % possible obs: 98.6 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 4151 / CC1/2: 0.648

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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: 1.4→45.379 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 1939 4.28 %
Rwork0.1638 82628 -
obs0.1646 45429 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.11 Å2 / Biso mean: 24.2464 Å2 / Biso min: 10.2 Å2
Refinement stepCycle: final / Resolution: 1.4→45.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 100 330 2115
Biso mean--18.97 33.25 -
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 (%)
1.4-1.41840.40111370.3577276286
1.4184-1.43790.33891240.3361293692
1.4379-1.45840.32071260.3203317297
1.4584-1.48020.35851700.30063208100
1.4802-1.50330.27021460.28223212100
1.5033-1.5280.29381470.25323248100
1.528-1.55430.3041170.23383210100
1.5543-1.58260.21961690.22123236100
1.5826-1.6130.21721350.19873237100
1.613-1.64590.25591530.19093217100
1.6459-1.68170.19741350.18643242100
1.6817-1.72080.16251510.17223240100
1.7208-1.76390.2391330.17053199100
1.7639-1.81160.17261540.16833252100
1.8116-1.86490.16261330.16243231100
1.8649-1.92510.22121490.1553317499
1.9251-1.99390.17121270.152324099
1.9939-2.07370.16931520.1435319399
2.0737-2.16810.17631520.1526315698
2.1681-2.28240.16391250.1466313297
2.2824-2.42540.19351350.1477311296
2.4254-2.61260.16171570.1434311196
2.6126-2.87550.14431400.1483229100
2.8755-3.29150.15571520.14623216100
3.2915-4.14650.14571410.1363236100
4.1465-45.3790.16981320.14283227100
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)
12.01564.2539-6.62322.0338-3.95347.79480.2215-0.67760.45060.3884-0.0976-0.1078-0.59380.4458-0.11250.1974-0.02080.00290.2172-0.02280.1955-25.92849.89912.9525
24.4190.46640.48734.4024-0.83292.4239-0.0328-0.0818-0.4684-0.0965-0.0411-0.25740.3650.19560.06830.16260.03730.02640.1787-0.00460.1065-18.6184-10.48866.1883
32.5939-1.2119-1.1164.16162.58844.2161-0.0251-0.0377-0.00180.08880.0699-0.0460.25660.1006-0.05810.10610.0124-0.00230.13330.04120.0688-26.7019-7.09086.6316
41.82060.353-0.66780.4867-0.70992.6334-0.00430.11260.0147-0.066-0.0175-0.00010.03060.03210.02010.12980.01280.0020.091-0.00850.13-28.00191.1341-11.769
53.45351.42381.00511.70150.75312.19280.0412-0.06630.18150.0605-0.04060.1485-0.0235-0.3535-0.00270.1130.02720.00120.1502-0.00130.1202-40.25914.3501-12.0611
65.4160.3164-1.43783.7443-0.41193.5574-0.0157-0.28620.34730.14020.00210.1137-0.2092-0.03240.01160.12370.0065-0.00230.0688-0.00650.0874-28.80688.001-5.9727
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 42 )A18 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 83 )A43 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 176 )A84 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 199 )A177 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 221 )A200 - 221

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