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- PDB-6b7c: Crystal structure of E.coli Phosphopantetheine Adenylyltransferas... -

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Basic information

Entry
Database: PDB / ID: 6b7c
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with N-((1,3-dimethyl-1H-pyrazol-5-yl)methyl)-5-methyl-1H-imidazo[4,5-b]pyridin-2-amine
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
Chem-CWP / DI(HYDROXYETHYL)ETHER / PYROPHOSPHATE 2- / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.564 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)39,60716
Polymers37,8052
Non-polymers1,80214
Water7,602422
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)118,82148
Polymers113,4166
Non-polymers5,40542
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_467z-1,-x+1,-y+21
crystal symmetry operation12_676-y+1,-z+2,x+11
Buried area24200 Å2
ΔGint-297 kcal/mol
Surface area34140 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-67 kcal/mol
Surface area14480 Å2
MethodPISA
3
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,13421
Polymers56,7083
Non-polymers2,42618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_467z-1,-x+1,-y+21
crystal symmetry operation12_676-y+1,-z+2,x+11
Buried area7470 Å2
ΔGint-92 kcal/mol
Surface area22490 Å2
MethodPISA
4
B: Phosphopantetheine adenylyltransferase
hetero molecules

B: Phosphopantetheine adenylyltransferase
hetero molecules

B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,68727
Polymers56,7083
Non-polymers2,97924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_467z-1,-x+1,-y+21
crystal symmetry operation12_676-y+1,-z+2,x+11
Buried area7620 Å2
ΔGint-94 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.050, 135.050, 135.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21B-492-

HOH

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
18ALAALAVALVAL(chain A and (resid 2 through 5 or resid 7...AA35 - 6735 - 67
19GLYGLYSERSER(chain A and (resid 2 through 5 or resid 7...AA69 - 7169 - 71
110LEULEULEULEU(chain A and (resid 2 through 5 or resid 7...AA7373
111ALAALAVALVAL(chain A and (resid 2 through 5 or resid 7...AA75 - 8575 - 85
112ILEILESERSER(chain A and (resid 2 through 5 or resid 7...AA87 - 11587 - 115
113PHEPHETRPTRP(chain A and (resid 2 through 5 or resid 7...AA117 - 124117 - 124
114ILEILESERSER(chain A and (resid 2 through 5 or resid 7...AA127 - 129127 - 129
115LEULEUVALVAL(chain A and (resid 2 through 5 or resid 7...AA131 - 142131 - 142
116HISHISVALVAL(chain A and (resid 2 through 5 or resid 7...AA144 - 160144 - 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
28ALAALAPROPRO(chain B and (resid 2 through 5 or resid 7...BB35 - 4035 - 40
29SERSERLYSLYS(chain B and (resid 2 through 5 or resid 7...BB41 - 4341 - 43
210GLNGLNVALVAL(chain B and (resid 2 through 5 or resid 7...BB2 - 1602 - 160
211GLNGLNVALVAL(chain B and (resid 2 through 5 or resid 7...BB2 - 1602 - 160
212GLNGLNVALVAL(chain B and (resid 2 through 5 or resid 7...BB2 - 1602 - 160
213GLNGLNVALVAL(chain B and (resid 2 through 5 or resid 7...BB2 - 1602 - 160

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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 , 6 types, 436 molecules

#2: Chemical ChemComp-CWP / N-[(1,3-dimethyl-1H-pyrazol-5-yl)methyl]-5-methyl-3H-imidazo[4,5-b]pyridin-2-amine


Mass: 256.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N6 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 57.27 %
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: 1.56→42.71 Å / Num. obs: 57669 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 20.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.016 / Rrim(I) all: 0.056 / Net I/σ(I): 21.7 / Num. measured all: 711585 / Scaling rejects: 158
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.56-1.5911.40.59428480.9130.1830.621100
8.57-42.71110.0238510.0060.02198.3

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Processing

Software
NameVersionClassification
Aimless0.5.29data 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: 1.564→26.485 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.12
RfactorNum. reflection% reflection
Rfree0.1985 2797 4.86 %
Rwork0.1734 --
obs0.1746 57578 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.9 Å2 / Biso mean: 27.2884 Å2 / Biso min: 12.8 Å2
Refinement stepCycle: final / Resolution: 1.564→26.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 109 422 3010
Biso mean--46.79 42.63 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072718
X-RAY DIFFRACTIONf_angle_d0.9623709
X-RAY DIFFRACTIONf_chiral_restr0.059413
X-RAY DIFFRACTIONf_plane_restr0.006470
X-RAY DIFFRACTIONf_dihedral_angle_d17.7131624
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1202X-RAY DIFFRACTION14.745TORSIONAL
12B1202X-RAY DIFFRACTION14.745TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.564-1.5910.25351140.233227712885100
1.591-1.61990.23941450.221426772822100
1.6199-1.65110.25821190.216327542873100
1.6511-1.68480.23321680.211326982866100
1.6848-1.72140.2411260.203827342860100
1.7214-1.76140.25371460.20126962842100
1.7614-1.80550.22921230.203527452868100
1.8055-1.85430.24561660.197627072873100
1.8543-1.90880.23581820.209426972879100
1.9088-1.97040.23721570.188726852842100
1.9704-2.04080.20681480.181827302878100
2.0408-2.12250.19921250.180927592884100
2.1225-2.2190.23871330.177227572890100
2.219-2.3360.17041470.16927152862100
2.336-2.48220.1951160.166627552871100
2.4822-2.67370.20341250.170827552880100
2.6737-2.94240.22471330.170327422875100
2.9424-3.36750.16991700.16832723289399
3.3675-4.23990.17371370.147827862923100
4.2399-26.48930.1681170.163628953012100
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)
10.07220.0561-0.03950.0393-0.110.06020.01-0.0608-0.03660.0255-0.07310.0115-0.02430.06-00.08820.01080.00420.1068-0.00170.093142.2642111.7181190.8311
20.42550.1236-0.49470.2694-0.06830.4037-0.0115-0.05650.022-0.0084-0.0590.0382-0.04910.1422-00.08070.0085-0.00350.1190.00230.088147.0071111.9785190.5734
30.43870.05610.120.1747-0.02440.3109-0.0304-0.0629-0.0107-0.0069-0.006-0.08620.0315-0.048500.096-0.00330.00040.11490.00390.081238.6476110.5979194.5202
40.08870.0710.07040.0880.04410.05280.02350.0985-0.01230.00210.0096-0.0517-0.0527-0.036900.1702-0.0070.02960.1306-0.00250.156530.221102.8907183.3087
50.0382-0.09060.0020.0715-0.04620.00120.17850.02710.0902-0.0048-0.13260.01780.03420.071-00.11030.02680.01070.11670.01840.117730.2031111.6483187.9722
60.2127-0.0031-0.5548-0.0506-0.15530.29860.0526-0.0143-0.0237-0.0492-0.01570.0047-0.03190.0100.06090.0170.00150.1136-0.00360.103356.4965108.2083179.2683
70.46830.50030.01840.7512-0.1380.1211-0.051-0.0570.08280.0050.05480.1246-0.0252-0.0099-00.07090.0088-0.01050.0806-0.00010.136417.9202124.0756178.0412
80.46240.0188-0.1817-0.0351-0.06320.4562-0.00550.0629-0.0365-0.03460.00390.0275-0.0472-0.0092-00.121-0.0181-0.00460.09-0.00320.104131.7066121.7813174.5642
90.1140.33480.21750.37410.25250.1370.03990.01290.11060.0093-0.06190.02010.1011-0.0134-00.091-0.0094-0.00130.12430.00860.15398.4817111.2306172.6297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )A2 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 59 )A16 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 92 )A60 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 109 )A93 - 109
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 119 )A110 - 119
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 160 )A120 - 160
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 73 )B2 - 73
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 119 )B74 - 119
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 160 )B120 - 160

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