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- PDB-6b7b: Crystal structure of E.coli Phosphopantetheine Adenylyltransferas... -

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Basic information

Entry
Database: PDB / ID: 6b7b
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 5-methoxy-2-methyl-1H-indole
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / CoaD
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-methoxy-2-methyl-1H-indole / PYROPHOSPHATE 2- / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsProudfoot, A.W. / Bussiere, D. / Lingel, A.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: High-Confidence Protein-Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization.
Authors: Proudfoot, A. / Bussiere, D.E. / Lingel, A.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,84411
Polymers37,8052
Non-polymers1,0399
Water6,341352
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,53333
Polymers113,4166
Non-polymers3,11727
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area21190 Å2
ΔGint-324 kcal/mol
Surface area33000 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-81 kcal/mol
Surface area14160 Å2
MethodPISA
3
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)466,132132
Polymers453,66524
Non-polymers12,467108
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_456-x-1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_465z-1,x+1,y1
crystal symmetry operation6_456z-1,-x,-y+11
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_566-z,x+1,-y+11
crystal symmetry operation9_456y-1,z,x+11
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_465y-1,-z+1,-x1
crystal symmetry operation12_566-y,-z+1,x+11
crystal symmetry operation13_455x-1/2,y+1/2,z+1/21
crystal symmetry operation14_455-x-1/2,-y+1/2,z+1/21
crystal symmetry operation15_455-x-1/2,y+1/2,-z+1/21
crystal symmetry operation16_455x-1/2,-y+1/2,-z+1/21
crystal symmetry operation17_455z-1/2,x+1/2,y+1/21
crystal symmetry operation18_455z-1/2,-x+1/2,-y+1/21
crystal symmetry operation19_455-z-1/2,-x+1/2,y+1/21
crystal symmetry operation20_455-z-1/2,x+1/2,-y+1/21
crystal symmetry operation21_455y-1/2,z+1/2,x+1/21
crystal symmetry operation22_455-y-1/2,z+1/2,-x+1/21
crystal symmetry operation23_455y-1/2,-z+1/2,-x+1/21
crystal symmetry operation24_455-y-1/2,-z+1/2,x+1/21
Buried area74120 Å2
ΔGint-917 kcal/mol
Surface area142630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.850, 134.850, 134.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 5 or resid 7...
21(chain B and (resid 2 through 5 or resid 7...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNALAALA(chain A and (resid 2 through 5 or resid 7...AA2 - 52 - 5
12TYRTYRGLYGLY(chain A and (resid 2 through 5 or resid 7...AA7 - 97 - 9
13PHEPHEHISHIS(chain A and (resid 2 through 5 or resid 7...AA11 - 1811 - 18
14ILEILETHRTHR(chain A and (resid 2 through 5 or resid 7...AA21 - 2321 - 23
15ALAALATHRTHR(chain A and (resid 2 through 5 or resid 7...AA25 - 2625 - 26
16PHEPHEPHEPHE(chain A and (resid 2 through 5 or resid 7...AA2929
17HISHISILEILE(chain A and (resid 2 through 5 or resid 7...AA31 - 3331 - 33
18ALAALAPROPRO(chain A and (resid 2 through 5 or resid 7...AA35 - 4435 - 44
19PHEPHETHRTHR(chain A and (resid 2 through 5 or resid 7...AA46 - 4746 - 47
110GLUGLUVALVAL(chain A and (resid 2 through 5 or resid 7...AA49 - 6749 - 67
111GLYGLYLEULEU(chain A and (resid 2 through 5 or resid 7...AA69 - 7369 - 73
112ALAALAILEILE(chain A and (resid 2 through 5 or resid 7...AA75 - 8775 - 87
113GLYGLYALAALA(chain A and (resid 2 through 5 or resid 7...AA89 - 9489 - 94
114PHEPHEGLUGLU(chain A and (resid 2 through 5 or resid 7...AA96 - 9996 - 99
115LEULEUSERSER(chain A and (resid 2 through 5 or resid 7...AA102 - 115102 - 115
116PHEPHEPHEPHE(chain A and (resid 2 through 5 or resid 7...AA117117
117METMETTRPTRP(chain A and (resid 2 through 5 or resid 7...AA119 - 124119 - 124
118ILEILESERSER(chain A and (resid 2 through 5 or resid 7...AA127 - 129127 - 129
119LEULEUALAALA(chain A and (resid 2 through 5 or resid 7...AA131 - 136131 - 136
120HISHISPROPRO(chain A and (resid 2 through 5 or resid 7...AA138 - 147138 - 147
121GLUGLUGLUGLU(chain A and (resid 2 through 5 or resid 7...AA148148
122METMETVALVAL(chain A and (resid 2 through 5 or resid 7...AA1 - 1601 - 160
123METMETVALVAL(chain A and (resid 2 through 5 or resid 7...AA1 - 1601 - 160
124METMETVALVAL(chain A and (resid 2 through 5 or resid 7...AA1 - 1601 - 160
125METMETVALVAL(chain A and (resid 2 through 5 or resid 7...AA1 - 1601 - 160
126METMETVALVAL(chain A and (resid 2 through 5 or resid 7...AA1 - 1601 - 160
21GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 52 - 5
22TYRTYRGLYGLY(chain B and (resid 2 through 5 or resid 7...BB7 - 97 - 9
23PHEPHEHISHIS(chain B and (resid 2 through 5 or resid 7...BB11 - 1811 - 18
24ILEILETHRTHR(chain B and (resid 2 through 5 or resid 7...BB21 - 2321 - 23
25ALAALATHRTHR(chain B and (resid 2 through 5 or resid 7...BB25 - 2625 - 26
26PHEPHEPHEPHE(chain B and (resid 2 through 5 or resid 7...BB2929
27HISHISILEILE(chain B and (resid 2 through 5 or resid 7...BB31 - 3331 - 33
28ALAALASERSER(chain B and (resid 2 through 5 or resid 7...BB35 - 3935 - 39
29LYSLYSPROPRO(chain B and (resid 2 through 5 or resid 7...BB43 - 4443 - 44
210PHEPHETHRTHR(chain B and (resid 2 through 5 or resid 7...BB46 - 4746 - 47
211GLUGLUVALVAL(chain B and (resid 2 through 5 or resid 7...BB49 - 6749 - 67
212GLYGLYLEULEU(chain B and (resid 2 through 5 or resid 7...BB69 - 7369 - 73
213ALAALAILEILE(chain B and (resid 2 through 5 or resid 7...BB75 - 8775 - 87
214GLYGLYLEULEU(chain B and (resid 2 through 5 or resid 7...BB89 - 9089 - 90
215ARGARGARGARG(chain B and (resid 2 through 5 or resid 7...BB9191
216GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 1592 - 159
217GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 1592 - 159
218GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 1592 - 159
219GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 1592 - 159
220GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 1592 - 159
221GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 1592 - 159
222GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 1592 - 159
223GLNGLNALAALA(chain B and (resid 2 through 5 or resid 7...BB2 - 1592 - 159

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 18902.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: coaD, kdtB, yicA, b3634, JW3609 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6I6, pantetheine-phosphate adenylyltransferase

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Non-polymers , 5 types, 361 molecules

#2: Chemical ChemComp-CWJ / 5-methoxy-2-methyl-1H-indole


Mass: 161.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.8 M AMMONIUM SULFATE, 0.25 M POTASSIUM THIOCYANATE, 0.2 M POTASSIUM BROMIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→47.68 Å / Num. obs: 28483 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 23.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.029 / Rrim(I) all: 0.083 / Net I/σ(I): 18.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.98-2.037.80.44319950.9080.1690.475100
9.07-47.687.20.0232010.0080.02297.6

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
iMOSFLM7.2.1data reduction
PHENIX1.12_2829phasing
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JBN

5jbn


Resolution: 1.981→28.75 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 18.31
RfactorNum. reflection% reflection
Rfree0.1966 1448 5.09 %
Rwork0.1768 --
obs0.1778 28454 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.66 Å2 / Biso mean: 27.3312 Å2 / Biso min: 9.35 Å2
Refinement stepCycle: final / Resolution: 1.981→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 73 352 2883
Biso mean--47.05 43.39 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042694
X-RAY DIFFRACTIONf_angle_d0.7633683
X-RAY DIFFRACTIONf_chiral_restr0.047415
X-RAY DIFFRACTIONf_plane_restr0.004468
X-RAY DIFFRACTIONf_dihedral_angle_d19.41627
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1070X-RAY DIFFRACTION7.903TORSIONAL
12B1070X-RAY DIFFRACTION7.903TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9809-2.05170.22191750.207826862861
2.0517-2.13390.19971370.203826442781
2.1339-2.23090.23651290.192727112840
2.2309-2.34850.20021480.185626592807
2.3485-2.49560.221550.185126802835
2.4956-2.68810.21881580.188926592817
2.6881-2.95840.18711300.179427182848
2.9584-3.38590.17111230.173227182841
3.3859-4.26360.16591360.155627332869
4.2636-28.75310.20721570.170527982955
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)
10.00470.00570.00550.0020.00360.0057-0.064-0.0633-0.0181-0.0011-0.0703-0.04820.0345-0.04070-0.1222-0.0025-0.09230.1195-0.04090.0024-45.744722.509955.4731
2-0.00060.001-0.0016-0.00020.00050.0028-0.0087-0.02260.00090.01540.0088-0.00280.0086-0.0016-00.07830.00020.00420.1726-0.02390.0625-39.234624.130462.4188
30.00190.0002-0.00130.0002-0.00060.00030.02290.02180.0101-0.014-0.00850.002-0.0129-0.0064-00.0799-0.00340.01310.0888-0.01480.0805-31.871927.702149.2236
40.0019-0.00060.0035-0.0020.00040.001-0.0032-0.03550.0513-0.0057-0.02130.0035-0.0009-0.01280-0.08530.037-0.01650.1383-0.03350.0797-56.049926.962244.0764
50.00220.0070.00480.00680.0031-0.0003-0.0179-0.0521-0.02020.00370.0325-0.07930.0364-0.0135-0-0.003-0.07880.0128-0.0968-0.01570.1271-17.738611.01142.6052
60.0041-0.00020.0043-0.00040.00270.00410.03430.00560.0355-0.01150.0005-0.01810.0289-0.005900.1325-0.00820.00450.038-0.00470.079-31.579913.226939.2226
70.00210.0052-0.00030.0037-0.00210.0004-0.01470.0084-0.02120.0139-0.0089-0.017-0.0332-0.001-00.0207-0.05240.00910.067-0.01370.1779-8.540623.85237.2196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 59 )A1 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 84 )A60 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 119 )A85 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 160 )A120 - 160
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 73 )B2 - 73
6X-RAY DIFFRACTION6chain 'B' and (resid 74 through 119 )B74 - 119
7X-RAY DIFFRACTION7chain 'B' and (resid 120 through 159 )B120 - 159

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