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- PDB-8gkf: Phosphopantetheinyl transferase PptT from Mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 8gkf
TitlePhosphopantetheinyl transferase PptT from Mycobacterium tuberculosis in complex with Raltitrexed.
Components4'-phosphopantetheinyl transferase PptT
KeywordsTRANSFERASE / complex / inhibitor / drug / Structural Genomics / TB Structural Genomics Consortium / TBSGC
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
TOMUDEX / 4'-phosphopantetheinyl transferase PptT
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKrieger, I.V. / Singh, A. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-040487 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AIO95208 United States
Welch FoundationA-0015 United States
CitationJournal: Sci Adv / Year: 2024
Title: Redirecting raltitrexed from cancer cell thymidylate synthase to Mycobacterium tuberculosis phosphopantetheinyl transferase.
Authors: Singh, A. / Ottavi, S. / Krieger, I. / Planck, K. / Perkowski, A. / Kaneko, T. / Davis, A.M. / Suh, C. / Zhang, D. / Goullieux, L. / Alex, A. / Roubert, C. / Gardner, M. / Preston, M. / ...Authors: Singh, A. / Ottavi, S. / Krieger, I. / Planck, K. / Perkowski, A. / Kaneko, T. / Davis, A.M. / Suh, C. / Zhang, D. / Goullieux, L. / Alex, A. / Roubert, C. / Gardner, M. / Preston, M. / Smith, D.M. / Ling, Y. / Roberts, J. / Cautain, B. / Upton, A. / Cooper, C.B. / Serbina, N. / Tanvir, Z. / Mosior, J. / Ouerfelli, O. / Yang, G. / Gold, B.S. / Rhee, K.Y. / Sacchettini, J.C. / Fotouhi, N. / Aube, J. / Nathan, C.
History
DepositionMar 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4'-phosphopantetheinyl transferase PptT
B: 4'-phosphopantetheinyl transferase PptT
C: 4'-phosphopantetheinyl transferase PptT
D: 4'-phosphopantetheinyl transferase PptT
E: 4'-phosphopantetheinyl transferase PptT
F: 4'-phosphopantetheinyl transferase PptT
G: 4'-phosphopantetheinyl transferase PptT
H: 4'-phosphopantetheinyl transferase PptT
I: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,07118
Polymers230,9449
Non-polymers4,1269
Water1,35175
1
A: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1192
Polymers25,6601
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.830, 141.830, 209.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-404-

HOH

21B-419-

HOH

31B-420-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 56 and (name N or name...
d_2ens_1(chain "B" and ((resid 56 and (name N or name...
d_3ens_1(chain "C" and ((resid 56 and (name N or name...
d_4ens_1(chain "D" and ((resid 56 and (name N or name...
d_5ens_1(chain "E" and ((resid 56 and (name N or name...
d_6ens_1(chain "G" and ((resid 56 and (name N or name...
d_7ens_1(chain "H" and ((resid 56 and (name N or name...
d_8ens_1(chain "I" and ((resid 56 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGPROA48 - 62
d_12ens_1ILEASPA65 - 69
d_13ens_1PROASPA76 - 77
d_14ens_1VALILEA80 - 121
d_15ens_1LEULEUA144
d_16ens_1ALATHRA150 - 151
d_17ens_1LEULEUA158
d_18ens_1ARGTRPA161 - 162
d_19ens_1SERSERA176
d_110ens_1VALVALA184
d_111ens_1ARGARGA186
d_112ens_1LEUALAA214 - 220
d_21ens_1ARGPROC50 - 64
d_22ens_1ILEASPC67 - 71
d_23ens_1PROASPC78 - 79
d_24ens_1VALILEC82 - 123
d_25ens_1LEULEUC146
d_26ens_1ALATHRC152 - 153
d_27ens_1LEULEUC160
d_28ens_1ARGTRPC163 - 164
d_29ens_1SERSERC178
d_210ens_1VALVALC186
d_211ens_1ARGARGC188
d_212ens_1LEUALAC216 - 222
d_31ens_1ARGPROE52 - 66
d_32ens_1ILEASPE69 - 73
d_33ens_1PROASPE80 - 81
d_34ens_1VALILEE84 - 125
d_35ens_1LEULEUE148
d_36ens_1ALATHRE154 - 155
d_37ens_1LEULEUE162
d_38ens_1ARGTRPE165 - 166
d_39ens_1SERSERE180
d_310ens_1VALVALE188
d_311ens_1ARGARGE190
d_312ens_1LEUALAE218 - 224
d_41ens_1ARGPROG52 - 66
d_42ens_1ILEASPG69 - 73
d_43ens_1PROASPG80 - 81
d_44ens_1VALILEG84 - 125
d_45ens_1LEULEUG148
d_46ens_1ALATHRG154 - 155
d_47ens_1LEULEUG162
d_48ens_1ARGTRPG165 - 166
d_49ens_1SERSERG180
d_410ens_1VALVALG188
d_411ens_1ARGARGG190
d_412ens_1LEUALAG218 - 224
d_51ens_1ARGPROI50 - 64
d_52ens_1ILEASPI67 - 71
d_53ens_1PROASPI78 - 79
d_54ens_1VALILEI82 - 123
d_55ens_1LEULEUI146
d_56ens_1ALATHRI152 - 153
d_57ens_1LEULEUI160
d_58ens_1ARGTRPI163 - 164
d_59ens_1SERSERI178
d_510ens_1VALVALI186
d_511ens_1ARGARGI188
d_512ens_1LEUALAI216 - 222
d_61ens_1ARGPROM47 - 61
d_62ens_1ILEASPM64 - 68
d_63ens_1PROASPM75 - 76
d_64ens_1VALILEM79 - 120
d_65ens_1LEULEUM126
d_66ens_1ALATHRM132 - 133
d_67ens_1LEULEUM140
d_68ens_1ARGTRPM143 - 144
d_69ens_1SERSERM158
d_610ens_1VALVALM166
d_611ens_1ARGARGM168
d_612ens_1LEUALAM190 - 196
d_71ens_1ARGASPO47 - 66
d_72ens_1PROILEO73 - 116
d_73ens_1LEUARGO194 - 198
d_74ens_1TRPVALO201 - 203
d_75ens_1ARGARGO205
d_76ens_1LEULEUO207
d_77ens_1THRALAO210 - 215
d_81ens_1ARGPROQ44 - 58
d_82ens_1ILEASPQ61 - 65
d_83ens_1PROASPQ72 - 73
d_84ens_1VALILEQ76 - 117
d_85ens_1LEULEUQ140
d_86ens_1ALATHRQ146 - 147
d_87ens_1LEULEUQ154
d_88ens_1ARGTRPQ157 - 158
d_89ens_1SERSERQ172
d_810ens_1VALVALQ180
d_811ens_1ARGARGQ182
d_812ens_1LEUALAQ210 - 216

NCS oper:
IDCodeMatrixVector
1given(-0.996455948817, -0.062610932923, -0.0561730642356), (-0.0615433583428, 0.997893051381, -0.0205395484326), (0.0573407107647, -0.0170096762002, -0.998209754413)-69.3686994555, 21.5225107105, 55.1686854187
2given(0.994011221863, 0.0976412220004, 0.0490701801075), (-0.0988969914259, 0.994811949173, 0.0238447241362), (-0.0464873735161, -0.028554816555, 0.998510664217)46.6132703112, -2.00761495594, -2.01452003206
3given(-0.105851854152, 0.993488527122, 0.0421418016979), (0.992902266047, 0.103288304643, 0.0589628374701), (0.0542261473011, 0.0480840160734, -0.997370268429)-49.9449579684, 45.0655881671, 2.59363162436
4given(-0.999767229153, 0.00434034252582, -0.021134070567), (0.00405069846528, 0.999897552738, 0.0137286514645), (0.0211914924891, 0.0136398480874, -0.999682387156)-118.103311001, -21.0075966404, 52.7314943562
5given(0.191304641817, -0.981009170147, -0.0319928446265), (0.980903330616, 0.18991555837, 0.0419611329241), (-0.0350883172372, -0.0394092473543, 0.998606890231)-64.9489621487, 22.6237055839, 50.1736397145
6given(0.997579252703, 0.0681800624875, 0.0136789493547), (-0.0694295686908, 0.987570521268, 0.14101063972), (-0.00389481291708, -0.141619012149, 0.98991357493)-49.2455376465, -49.8933179966, 1.04066923183
7given(-0.995413478267, -0.0810213495335, -0.0508679486876), (-0.0813822085098, 0.99667012252, 0.00505994210671), (0.0502886013127, 0.00917648057883, -0.998692569704)-70.8346190171, -27.5162742515, 55.205866479

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Components

#1: Protein
4'-phosphopantetheinyl transferase PptT / PPTase


Mass: 25660.471 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pptT, Rv2794c / Production host: Escherichia coli (E. coli)
References: UniProt: O33336, holo-[acyl-carrier-protein] synthase
#2: Chemical
ChemComp-D16 / TOMUDEX / ZD1694 / Raltitrexed / Raltitrexed


Mass: 458.488 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H22N4O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: K/Na Tartrate, imidazole buffer pH 8.0, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.44→117.49 Å / Num. obs: 86872 / % possible obs: 94.5 % / Redundancy: 13.6 % / Biso Wilson estimate: 39.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.073 / Rrim(I) all: 0.291 / Net I/σ(I): 8.3
Reflection shellResolution: 2.448→2.558 Å / Rmerge(I) obs: 2.086 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4279 / CC1/2: 0.541 / Rpim(I) all: 0.593 / Rrim(I) all: 2.17

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→21.08 Å / SU ML: 0.4206 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3258 3604 5.01 %
Rwork0.2815 68284 -
obs0.2837 71888 90.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.97 Å2
Refinement stepCycle: LAST / Resolution: 2.45→21.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13905 0 288 75 14268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005914561
X-RAY DIFFRACTIONf_angle_d0.997119904
X-RAY DIFFRACTIONf_chiral_restr0.06612253
X-RAY DIFFRACTIONf_plane_restr0.0082553
X-RAY DIFFRACTIONf_dihedral_angle_d17.9695300
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.286489328427
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.49025210734
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.435844614097
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.348335420055
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.561084049714
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS5.98797399874
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.5261434217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.4027320.3434566X-RAY DIFFRACTION19.88
2.48-2.510.3881460.339969X-RAY DIFFRACTION34.11
2.51-2.550.4116720.3241524X-RAY DIFFRACTION53.58
2.55-2.590.38951320.34672118X-RAY DIFFRACTION74.8
2.59-2.630.4011590.33162562X-RAY DIFFRACTION90.88
2.63-2.670.38651400.34712776X-RAY DIFFRACTION97.14
2.67-2.720.33071650.33322837X-RAY DIFFRACTION99.5
2.72-2.770.38541460.33842831X-RAY DIFFRACTION100
2.77-2.820.35731490.33362877X-RAY DIFFRACTION100
2.82-2.880.40751300.31872878X-RAY DIFFRACTION99.97
2.88-2.940.32941420.31762855X-RAY DIFFRACTION99.97
2.94-3.010.35181520.31792858X-RAY DIFFRACTION100
3.01-3.080.36221690.3022869X-RAY DIFFRACTION99.93
3.08-3.170.34761640.2952850X-RAY DIFFRACTION99.93
3.17-3.260.35931540.30442849X-RAY DIFFRACTION99.9
3.26-3.360.341590.29762865X-RAY DIFFRACTION99.97
3.36-3.480.35981400.28622883X-RAY DIFFRACTION99.8
3.48-3.620.36721320.27232922X-RAY DIFFRACTION99.93
3.62-3.790.29851630.27212855X-RAY DIFFRACTION99.9
3.79-3.980.28381730.24732878X-RAY DIFFRACTION99.93
3.98-4.230.27171390.23962920X-RAY DIFFRACTION99.61
4.23-4.560.27211390.23322921X-RAY DIFFRACTION99.74
4.56-5.010.2871300.24052936X-RAY DIFFRACTION99.55
5.01-5.720.2871680.25862923X-RAY DIFFRACTION99.49
5.72-7.160.36891500.28392998X-RAY DIFFRACTION99.65
7.16-21.080.2891590.28092964X-RAY DIFFRACTION94.75

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