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- PDB-8qzh: Crystal structure of apo-PptT from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8qzh
TitleCrystal structure of apo-PptT from Mycobacterium tuberculosis
Components4'-phosphopantetheinyl transferase PptT
KeywordsTRANSFERASE
Function / homology
Function and homology information


siderophore metabolic process / enterobactin synthetase complex / holo-[acyl-carrier-protein] synthase / enterobactin biosynthetic process / siderophore 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
ACETATE ION / 4'-phosphopantetheinyl transferase PptT
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGavalda, S. / Carivenc, C. / Mourey, L. / Pedelacq, J.D.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)09-BLAN-0298-01 France
CitationJournal: Acs Catalysis / Year: 2024
Title: Catalytic Cycle of Type II 4'-Phosphopantetheinyl Transferases
Authors: Gavalda, S. / Faille, A. / Fioccola, S. / Nguyen, M.C. / Carivenc, C. / Rottier, K. / Rufin, Y. / Saitta, S. / Czaplicki, G. / Guilhot, C. / Chalut, C. / Brut, M. / Mourey, L. / Pedelacq, J.D.
History
DepositionOct 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,1597
Polymers26,9091
Non-polymers2506
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-25 kcal/mol
Surface area11070 Å2
Unit cell
Length a, b, c (Å)46.169, 46.169, 181.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein 4'-phosphopantetheinyl transferase PptT


Mass: 26908.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pptT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O33336
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 3M Mg acetate 0.1M Na acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.7→60.59 Å / Num. obs: 23986 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 25.75 Å2 / CC1/2: 0.944 / Net I/σ(I): 3.3
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 2366 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata processing
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.99 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.9121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 2076 4.39 %
Rwork0.2059 45213 -
obs0.2072 23969 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 15 138 1951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381878
X-RAY DIFFRACTIONf_angle_d0.71642567
X-RAY DIFFRACTIONf_chiral_restr0.045291
X-RAY DIFFRACTIONf_plane_restr0.0041334
X-RAY DIFFRACTIONf_dihedral_angle_d16.4185264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.36021330.35692769X-RAY DIFFRACTION92.33
1.74-1.780.29971390.34073020X-RAY DIFFRACTION98.56
1.78-1.830.37021340.30842987X-RAY DIFFRACTION99.68
1.83-1.890.33291340.29623016X-RAY DIFFRACTION99.87
1.89-1.950.25781420.28073054X-RAY DIFFRACTION100
1.95-2.020.26371400.25463068X-RAY DIFFRACTION100
2.02-2.10.30361430.24163038X-RAY DIFFRACTION99.97
2.1-2.190.22871380.23313020X-RAY DIFFRACTION100
2.19-2.310.24871400.22113071X-RAY DIFFRACTION99.88
2.31-2.450.25321400.21692996X-RAY DIFFRACTION100
2.45-2.640.23331270.20793041X-RAY DIFFRACTION99.94
2.64-2.910.21341420.20433029X-RAY DIFFRACTION99.94
2.91-3.330.24321440.18983044X-RAY DIFFRACTION100
3.33-4.190.20281400.16383042X-RAY DIFFRACTION99.94
4.19-39.980.1971400.16813018X-RAY DIFFRACTION99.97
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)
10.295476983938-0.148847843754-0.3552782907450.312796998277-0.01322884221150.515048949989-0.05557698203780.0718016087796-0.284331286950.1637575968560.18186779073-0.13757205839-0.270483554468-0.08433526025730.0002141958894280.3034326602230.00603452091091-0.01500269508140.3088951880880.04094589687150.330262710455-13.0437819225-2.593395883294.86179428244
20.739791435882-0.6185570298140.4387612309530.543696045053-0.3931471798731.13782279780.0275216614119-0.03004819328720.123602359853-0.0111321889651-0.0108908430941-0.0503004107623-0.01873968106410.280309384934-0.0001502930988210.272074299386-0.03973410510320.008960311824170.396633515806-0.01378835472470.290974375838-0.575658266584-1.65405006951-9.89604247356
30.8059858791920.0640324256043-0.2479486854190.3090078599690.5830643113241.204158927040.0868171814611-0.1060090966340.1131510480830.252232538946-0.10234026719-0.161485227587-0.1994393325330.463331063048-1.37198033526E-60.233687664607-0.004420525062230.008503524353830.4731365743260.02726080743220.2935824514072.51328890519-1.79984639474-11.3552822748
40.3378171016710.0383282651754-0.303289461290.2543519915340.05187778652260.2803182256980.1387392928530.1165858378270.385945526977-0.692303354344-0.1190820286670.03903736885070.276584163533-0.0716650478-0.0003363923597640.3539192606430.052152511198-0.05281546961470.369787730591-0.01474542226020.319224884321-1.83103971763-4.83252924568-22.074556845
51.33632732403-0.567611302445-0.1195598193611.013137722290.1532210324461.602613446560.0617700231976-0.04386706905270.0180593559005-0.0368315922294-0.05350239115140.0425176063148-0.07433309974910.003264281690834.80776940428E-50.208599688493-0.02529246904560.007822802016320.217436644683-0.002037341210610.224560528198-16.01438019283.98255819224-13.3729494001
60.2245676605440.215031994992-0.04141302925240.2109021941440.04377101707310.3314536121710.2601971414530.37129441621-0.0867192254489-0.365918511534-0.1954071128180.0938191980520.129254770121-0.1667079884610.001174830426570.2776093924430.01767323501390.02527878145140.293476231240.01491070349210.26555402837-18.48824009131.49579687016-25.6928487184
70.07772435220560.1861622692280.0005689209700440.3981014047420.05258543575850.07478502004130.2036617186790.0240151934712-0.009194560458930.06602708937470.1406016591080.2124283506950.301930127129-0.279751830113-0.001541145897880.2427890927780.03975494267420.03994554888550.319423586161-0.03550853419390.290966852351-26.75287916664.12724053038-9.62671906783
80.736792750281-0.324709387901-0.2747176685910.680272158747-0.3651124840590.4595818487340.127141687575-0.00589458840628-0.09902693511340.159597848413-0.06145492445440.2385108076190.290227233929-0.3707589824440.0004926771548610.2280781823250.01648584754230.005316634923860.266841125779-0.0150548709320.271693870172-24.76689688761.68885392032-10.9548728577
90.1608822494640.1542072300220.1133746241210.1291826483230.1740533243140.1550550754420.0575312367807-0.0232377463249-0.1250164725460.4311820721580.0844235366860.06526757868360.754832609560.01025506129550.0002648146705960.3399269324890.0059720966392-0.02110325609690.244749909931-0.02554296137420.295586970073-22.7442856726-8.62357078589-18.6545976661
100.287521750327-0.107692277837-0.1303188387540.33786880405-0.1720396288440.2874410579960.125169580593-0.0198518897064-0.05946179625250.4816997129680.0753091526143-0.1763782663630.2081863279840.226397524406-0.000102916399560.2274176491850.00841834149985-0.007021138503040.223768290234-0.04744706087380.269821782518-15.04465826673.72328286476-4.76371541281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -8 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 167 )
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 184 )
8X-RAY DIFFRACTION8chain 'A' and (resid 185 through 198 )
9X-RAY DIFFRACTION9chain 'A' and (resid 199 through 213 )
10X-RAY DIFFRACTION10chain 'A' and (resid 214 through 227 )

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