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- PDB-6b7f: Crystal structure of E.coli Phosphopantetheine Adenylyltransferas... -

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Basic information

Entry
Database: PDB / ID: 6b7f
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-3,3-dimethyl-4-(5-vinyl-1H-imidazol-1-yl)isochroman-1-one
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-CW4 / : / PYROPHOSPHATE 2- / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.562 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)38,95112
Polymers37,8052
Non-polymers1,14610
Water2,936163
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)116,85436
Polymers113,4166
Non-polymers3,43830
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 area23430 Å2
ΔGint-336 kcal/mol
Surface area32380 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-88 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.780, 135.780, 135.780
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 3 through 5 or resid 7...
21(chain B and (resid 3 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
11LYSLYSALAALA(chain G and (resid 3 through 5 or resid 7...AA3 - 53 - 5
12TYRTYRTHRTHR(chain G and (resid 3 through 5 or resid 7...AA7 - 267 - 26
13PHEPHEPROPRO(chain G and (resid 3 through 5 or resid 7...AA29 - 4429 - 44
14PHEPHEALAALA(chain G and (resid 3 through 5 or resid 7...AA46 - 5846 - 58
15ALAALAASNASN(chain G and (resid 3 through 5 or resid 7...AA60 - 6460 - 64
16GLUGLUVALVAL(chain G and (resid 3 through 5 or resid 7...AA66 - 6766 - 67
17GLYGLYLEULEU(chain G and (resid 3 through 5 or resid 7...AA69 - 7369 - 73
18ALAALAALAALA(chain G and (resid 3 through 5 or resid 7...AA75 - 8375 - 83
19VALVALVALVAL(chain G and (resid 3 through 5 or resid 7...AA8585
110ILEILEGLUGLU(chain G and (resid 3 through 5 or resid 7...AA87 - 9987 - 99
111GLNGLNGLNGLN(chain G and (resid 3 through 5 or resid 7...AA101101
112ALAALASERSER(chain G and (resid 3 through 5 or resid 7...AA103 - 115103 - 115
113PHEPHETRPTRP(chain G and (resid 3 through 5 or resid 7...AA117 - 124117 - 124
114PHEPHEPROPRO(chain G and (resid 3 through 5 or resid 7...AA126 - 147126 - 147
115GLUGLUGLUGLU(chain G and (resid 3 through 5 or resid 7...AA148148
116GLNGLNVALVAL(chain G and (resid 3 through 5 or resid 7...AA2 - 1602 - 160
117GLNGLNVALVAL(chain G and (resid 3 through 5 or resid 7...AA2 - 1602 - 160
118GLNGLNVALVAL(chain G and (resid 3 through 5 or resid 7...AA2 - 1602 - 160
119GLNGLNVALVAL(chain G and (resid 3 through 5 or resid 7...AA2 - 1602 - 160
21LYSLYSALAALA(chain H and (resid 3 through 5 or resid 7...BB3 - 53 - 5
22TYRTYRTHRTHR(chain H and (resid 3 through 5 or resid 7...BB7 - 267 - 26
23PHEPHESERSER(chain H and (resid 3 through 5 or resid 7...BB29 - 4129 - 41
24LYSLYSLYSLYS(chain H and (resid 3 through 5 or resid 7...BB42 - 4342 - 43
25LYSLYSALAALA(chain H and (resid 3 through 5 or resid 7...BB3 - 1593 - 159
26LYSLYSALAALA(chain H and (resid 3 through 5 or resid 7...BB3 - 1593 - 159
27LYSLYSALAALA(chain H and (resid 3 through 5 or resid 7...BB3 - 1593 - 159
28LYSLYSALAALA(chain H and (resid 3 through 5 or resid 7...BB3 - 1593 - 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 , 7 types, 173 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CW4 / (4R)-4-(5-ethenyl-1H-imidazol-1-yl)-3,3-dimethyl-3,4-dihydro-1H-2-benzopyran-1-one


Mass: 268.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
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: 2.56→67.89 Å / Num. obs: 13570 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 41.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.03 / Rrim(I) all: 0.101 / Net I/σ(I): 19.3 / Num. measured all: 149733 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.56-2.68110.5941809616470.9120.1870.6234.2100
8.87-67.899.90.019360336410.0060.0248.599.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.31data scaling
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: 2.562→30.361 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 639 4.72 %
Rwork0.1772 12897 -
obs0.1787 13536 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.06 Å2 / Biso mean: 45.0419 Å2 / Biso min: 16.42 Å2
Refinement stepCycle: final / Resolution: 2.562→30.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 66 163 2684
Biso mean--60.11 49.09 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072608
X-RAY DIFFRACTIONf_angle_d0.9943556
X-RAY DIFFRACTIONf_chiral_restr0.056406
X-RAY DIFFRACTIONf_plane_restr0.006450
X-RAY DIFFRACTIONf_dihedral_angle_d19.6141557
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1218X-RAY DIFFRACTION10.503TORSIONAL
12B1218X-RAY DIFFRACTION10.503TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5623-2.76010.30011300.225425312661
2.7601-3.03760.26631430.213825352678
3.0376-3.47660.2541240.190725902714
3.4766-4.3780.17261190.156925942713
4.378-30.36340.16871230.16226472770
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)
10.0013-0.0545-0.0092-0.0382-0.0420.0333-0.116-0.3967-0.18980.0909-0.3461-0.171-0.0171-0.009400.24440.03580.01450.4226-0.06450.238842.877112.0751191.2622
20.08490.0104-0.0072-0.0013-0.08360.021-0.0762-0.420.2887-0.31390.0233-0.2252-0.18950.348100.20970.038-0.01490.3183-0.0770.304842.536118.1879189.1851
30.0010.00660.0023-0.0083-0.01380.01170.2449-0.01080.09590.1895-0.1071-0.19440.17470.0802-00.47730.10360.08840.50370.07950.301151.51299.4201191.1578
40.00770.0043-0.015-0.00140.01760.0222-0.5056-0.28870.39160.0022-0.26680.2355-0.19010.1633-00.16470.01820.04730.6339-0.0560.326353.5744111.1848194.7149
50.2108-0.12490.15240.056-0.02-0.0054-0.0548-0.5026-0.1882-0.21450.1841-0.3011-0.2485-0.3345-00.20280.0274-0.04010.56020.02140.256638.8482111.716194.7697
60.04480.07480.04790.14120.11510.03040.33610.1452-0.3023-0.2831-0.61010.04280.33270.1752-00.38550.1207-0.05140.31920.07140.239830.7216103.8694184.3455
70.01860.02590.01140.00170.0164-0.00020.3581-0.15810.0149-0.0375-0.1097-0.24760.0114-0.0138-00.180.0308-0.01490.30570.04070.249230.5466112.5261188.7198
80.00890.01450.0132-0.0031-0.0102-0.0065-0.34980.1988-0.1071-0.1733-0.1319-0.0738-0.35940.065500.20140.03460.04170.50080.01190.390346.7862114.0501174.8598
90.0079-0.00020.00270.00250.00460.00080.04050.2595-0.1507-0.02540.1894-0.27980.01770.186900.2324-0.0011-0.0280.26060.0750.27955.1432102.472178.8589
100.004-0.0684-0.0196-0.0468-0.02710.0124-0.1823-0.16730.14940.0897-0.01120.17310.09530.509400.18190.0669-0.00920.35930.07750.222161.2818108.5719182.4967
110.08520.1390.04560.28310.12660.076-0.0262-0.0624-0.01490.04750.03180.1192-0.05630.0356-00.1772-0.0016-0.02740.16570.00810.244617.6421123.6445177.8683
12-0.0079-0.0197-0.00730.0040.04650.0133-0.27720.21690.27390.03710.2680.0986-0.16280.2038-00.23020.32220.1749-0.2072-0.14520.234718.7359129.1948180.3615
130.19850.02260.07530.05030.05950.0480.03180.0017-0.0314-0.0396-0.04780.1544-0.07570.163600.30330.0338-0.0360.168-0.00290.286831.7796122.5574175.225
140.0460.17560.03870.1647-0.0956-0.0071-0.01450.24390.45650.1782-0.38520.13150.55460.207300.1716-0.0295-0.02710.21870.01930.34088.6044111.964173.3462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )A - G2 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 37 )A - G16 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 47 )A - G38 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 59 )A - G48 - 59
5X-RAY DIFFRACTION5chain 'A' and (resid 60 through 92 )A - G60 - 92
6X-RAY DIFFRACTION6chain 'A' and (resid 93 through 109 )A - G93 - 109
7X-RAY DIFFRACTION7chain 'A' and (resid 110 through 119 )A - G110 - 119
8X-RAY DIFFRACTION8chain 'A' and (resid 120 through 128 )A - G120 - 128
9X-RAY DIFFRACTION9chain 'A' and (resid 129 through 137 )A - G129 - 137
10X-RAY DIFFRACTION10chain 'A' and (resid 138 through 160 )A - G138 - 160
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 59 )B - H3 - 59
12X-RAY DIFFRACTION12chain 'B' and (resid 60 through 73 )B - H60 - 73
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 119 )B - H74 - 119
14X-RAY DIFFRACTION14chain 'B' and (resid 120 through 159 )B - H120 - 159

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