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- PDB-6b7e: Crystal structure of E.coli Phosphopantetheine Adenylyltransferas... -

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Basic information

Entry
Database: PDB / ID: 6b7e
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-4-(5-(difluoromethyl)-1H-imidazol-1-yl)-3,3-dimethylisochroman-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-CWA / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.104 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)38,92612
Polymers37,8052
Non-polymers1,12110
Water5,513306
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)116,77936
Polymers113,4166
Non-polymers3,36330
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_366z-2,x+1,y+11
crystal symmetry operation9_447y-1,z-1,x+21
Buried area22170 Å2
ΔGint-484 kcal/mol
Surface area33200 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-118 kcal/mol
Surface area14190 Å2
MethodPISA
3
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)467,117144
Polymers453,66524
Non-polymers13,452120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_559-x,y,-z+41
crystal symmetry operation4_579x,-y+2,-z+41
crystal symmetry operation5_366z-2,x+1,y+11
crystal symmetry operation6_368z-2,-x+1,-y+31
crystal symmetry operation7_766-z+2,-x+1,y+11
crystal symmetry operation8_768-z+2,x+1,-y+31
crystal symmetry operation9_447y-1,z-1,x+21
crystal symmetry operation10_647-y+1,z-1,-x+21
crystal symmetry operation11_487y-1,-z+3,-x+21
crystal symmetry operation12_687-y+1,-z+3,x+21
crystal symmetry operation13_444x-1/2,y-1/2,z-1/21
crystal symmetry operation14_574-x+1/2,-y+5/2,z-1/21
crystal symmetry operation15_549-x+1/2,y-1/2,-z+9/21
crystal symmetry operation16_479x-1/2,-y+5/2,-z+9/21
crystal symmetry operation17_255z-5/2,x+1/2,y+1/21
crystal symmetry operation18_268z-5/2,-x+3/2,-y+7/21
crystal symmetry operation19_765-z+5/2,-x+3/2,y+1/21
crystal symmetry operation20_758-z+5/2,x+1/2,-y+7/21
crystal symmetry operation21_336y-3/2,z-3/2,x+3/21
crystal symmetry operation22_637-y+3/2,z-3/2,-x+5/21
crystal symmetry operation23_387y-3/2,-z+7/2,-x+5/21
crystal symmetry operation24_686-y+3/2,-z+7/2,x+3/21
Buried area74550 Å2
ΔGint-1622 kcal/mol
Surface area146930 Å2
MethodPISA
4
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,80715
Polymers56,7083
Non-polymers1,09912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_366z-2,x+1,y+11
crystal symmetry operation9_447y-1,z-1,x+21
Buried area5690 Å2
ΔGint-162 kcal/mol
Surface area21970 Å2
MethodPISA
5
B: Phosphopantetheine adenylyltransferase
hetero molecules

B: Phosphopantetheine adenylyltransferase
hetero molecules

B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,97221
Polymers56,7083
Non-polymers2,26418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_366z-2,x+1,y+11
crystal symmetry operation9_447y-1,z-1,x+21
Buried area6770 Å2
ΔGint-222 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.480, 135.480, 135.480
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-450-

HOH

21B-450-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 and (name N or name...
21(chain B and (resid 2 through 9 or resid 11...

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
11GLNGLNGLNGLN(chain A and ((resid 2 and (name N or name...AA22
12GLNGLNVALVAL(chain A and ((resid 2 and (name N or name...AA2 - 1602 - 160
13GLNGLNVALVAL(chain A and ((resid 2 and (name N or name...AA2 - 1602 - 160
14GLNGLNVALVAL(chain A and ((resid 2 and (name N or name...AA2 - 1602 - 160
15GLNGLNVALVAL(chain A and ((resid 2 and (name N or name...AA2 - 1602 - 160
21GLNGLNGLYGLY(chain B and (resid 2 through 9 or resid 11...BB2 - 92 - 9
22PHEPHEILEILE(chain B and (resid 2 through 9 or resid 11...BB11 - 1911 - 19
23ILEILEPHEPHE(chain B and (resid 2 through 9 or resid 11...BB21 - 2921 - 29
24HISHISILEILE(chain B and (resid 2 through 9 or resid 11...BB31 - 3331 - 33
25ALAALAALAALA(chain B and (resid 2 through 9 or resid 11...BB35 - 3835 - 38
26SERSERSERSER(chain B and (resid 2 through 9 or resid 11...BB3939
27GLNGLNALAALA(chain B and (resid 2 through 9 or resid 11...BB2 - 1592 - 159
28GLNGLNALAALA(chain B and (resid 2 through 9 or resid 11...BB2 - 1592 - 159
29GLNGLNALAALA(chain B and (resid 2 through 9 or resid 11...BB2 - 1592 - 159
210GLNGLNALAALA(chain B and (resid 2 through 9 or resid 11...BB2 - 1592 - 159

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CWA / (4R)-4-[5-(difluoromethyl)-1H-imidazol-1-yl]-3,3-dimethyl-3,4-dihydro-1H-2-benzopyran-1-one


Mass: 292.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14F2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
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: Bruker Platinum 135 / Detector: CCD / 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: 2.1→36.21 Å / Num. obs: 23975 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 30.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.058 / Rrim(I) all: 0.125 / Net I/σ(I): 10.6 / Num. measured all: 106196 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.164.30.86517570.5580.4570.98499.2
9.41-36.214.20.0242740.9990.0120.02792.7

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
xia21.6data reduction
PHENIX1.12_2829phasing
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JBN

5jbn


Resolution: 2.104→30.294 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.68
RfactorNum. reflection% reflection
Rfree0.2062 1205 5.03 %
Rwork0.1714 --
obs0.1732 23970 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.33 Å2 / Biso mean: 34.2467 Å2 / Biso min: 16.32 Å2
Refinement stepCycle: final / Resolution: 2.104→30.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 64 306 2833
Biso mean--53.25 44.84 -
Num. residues----317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092640
X-RAY DIFFRACTIONf_angle_d0.9883606
X-RAY DIFFRACTIONf_chiral_restr0.059411
X-RAY DIFFRACTIONf_plane_restr0.007460
X-RAY DIFFRACTIONf_dihedral_angle_d17.8981583
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1262X-RAY DIFFRACTION14.079TORSIONAL
12B1262X-RAY DIFFRACTION14.079TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1036-2.18780.32691370.25632479261699
2.1878-2.28730.25521350.219725252660100
2.2873-2.40780.23751550.210225172672100
2.4078-2.55860.2671010.198625612662100
2.5586-2.75610.27341190.200925162635100
2.7561-3.03320.19541420.184225322674100
3.0332-3.47160.19411410.16722533267499
3.4716-4.37170.16961290.13732539266899
4.3717-30.29740.17321460.14432563270998
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)
1-0.2690.210.48250.4016-0.49920.2144-0.1230.0977-0.09070.1765-0.1101-0.0116-0.2248-0.10900.1903-0.02670.00570.09220.03390.150123.2742181.2414326.5255
20.12050.2883-0.14190.5681-0.08810.0669-0.03050.07620.00150.13410.11040.0147-0.05780.0685-00.17790.01570.00310.1398-0.01810.156226.3883170.5467325.6742
3-0.0930.02990.0190.202-0.17740.3009-0.01190.0295-0.05930.13030.0332-0.0617-0.05850.0095-00.1968-0.029-0.02980.11050.01180.184526.9875192.0773315.461
40.813-0.20650.02450.52690.11580.1048-0.0120.0131-0.11320.07470.08660.06380.0119-0.059800.09690.00140.00750.1289-0.0020.151110.6615155.6276313.4426
50.06020.173-0.00010.1371-0.04720.1282-0.06990.0096-0.0334-0.07050.0371-0.0557-0.0398-0.092500.128-0.00060.00710.1742-0.0150.159315.6578169.4459308.8446
60.4994-0.4928-0.14370.24090.17160.1313-0.0951-0.0217-0.10370.0026-0.07850.1627-0.05760.143700.15490.0158-0.00370.1348-0.01510.217523.8323144.2719308.7802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 58 )A2 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 119 )A59 - 119
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 160 )A120 - 160
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 92 )B2 - 92
5X-RAY DIFFRACTION5chain 'B' and (resid 93 through 118 )B93 - 118
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 159 )B119 - 159

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