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- PDB-6b7a: Crystal structure of E.coli Phosphopantetheine Adenylyltransferas... -

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Basic information

Entry
Database: PDB / ID: 6b7a
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 2-methyl-1H-benzo[d]imidazol-4-ol
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
2-methyl-1H-benzimidazol-7-ol / DI(HYDROXYETHYL)ETHER / PYROPHOSPHATE 2- / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.991 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)39,11214
Polymers37,8052
Non-polymers1,30612
Water6,612367
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)117,33642
Polymers113,4166
Non-polymers3,91936
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area23890 Å2
ΔGint-398 kcal/mol
Surface area33060 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-96 kcal/mol
Surface area14180 Å2
MethodPISA
3
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)469,342168
Polymers453,66524
Non-polymers15,677144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_456-x-1,y,-z+11
crystal symmetry operation4_546x,-y-1,-z+11
crystal symmetry operation5_456z-1,x,y+11
crystal symmetry operation6_445z-1,-x-1,-y1
crystal symmetry operation7_546-z,-x-1,y+11
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_546y,z-1,x+11
crystal symmetry operation10_445-y-1,z-1,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_456-y-1,-z,x+11
crystal symmetry operation13_445x-1/2,y-1/2,z+1/21
crystal symmetry operation14_445-x-1/2,-y-1/2,z+1/21
crystal symmetry operation15_445-x-1/2,y-1/2,-z+1/21
crystal symmetry operation16_445x-1/2,-y-1/2,-z+1/21
crystal symmetry operation17_445z-1/2,x-1/2,y+1/21
crystal symmetry operation18_445z-1/2,-x-1/2,-y+1/21
crystal symmetry operation19_445-z-1/2,-x-1/2,y+1/21
crystal symmetry operation20_445-z-1/2,x-1/2,-y+1/21
crystal symmetry operation21_445y-1/2,z-1/2,x+1/21
crystal symmetry operation22_445-y-1/2,z-1/2,-x+1/21
crystal symmetry operation23_445y-1/2,-z-1/2,-x+1/21
crystal symmetry operation24_445-y-1/2,-z-1/2,x+1/21
Buried area85660 Å2
ΔGint-1091 kcal/mol
Surface area142160 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)58,47221
Polymers56,7083
Non-polymers1,76418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area7020 Å2
ΔGint-121 kcal/mol
Surface area21540 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)58,86321
Polymers56,7083
Non-polymers2,15518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area7840 Å2
ΔGint-131 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.600, 134.600, 134.600
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
11B-484-

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 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
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
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
23PHEPHEILEILE(chain B and (resid 2 through 5 or resid 7...BB11 - 1911 - 19
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 - 4135 - 41
29LYSLYSLYSLYS(chain B and (resid 2 through 5 or resid 7...BB42 - 4342 - 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, 379 molecules

#2: Chemical ChemComp-CWM / 2-methyl-1H-benzimidazol-7-ol


Mass: 148.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


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


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
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: 1.99→47.59 Å / Num. obs: 27924 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.038 / Rrim(I) all: 0.107 / Net I/σ(I): 14.1 / Num. measured all: 212001 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.99-2.047.40.66119590.830.2590.711100
9.12-47.596.70.02531410.010.02797.3

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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: 1.991→28.697 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.97
RfactorNum. reflection% reflection
Rfree0.1986 1416 5.08 %
Rwork0.174 --
obs0.1752 27864 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.99 Å2 / Biso mean: 28.7915 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 1.991→28.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 78 368 2933
Biso mean--44.62 42.97 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052701
X-RAY DIFFRACTIONf_angle_d0.8593685
X-RAY DIFFRACTIONf_chiral_restr0.049415
X-RAY DIFFRACTIONf_plane_restr0.005496
X-RAY DIFFRACTIONf_dihedral_angle_d17.4581654
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1197X-RAY DIFFRACTION10.038TORSIONAL
12B1197X-RAY DIFFRACTION10.038TORSIONAL
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
1.9911-2.06220.21651610.212226052766
2.0622-2.14480.25321400.208426192759
2.1448-2.24230.22841410.194526282769
2.2423-2.36050.20611270.185926332760
2.3605-2.50830.23731630.187826182781
2.5083-2.70180.20671500.191126162766
2.7018-2.97350.20541260.180126632789
2.9735-3.40320.17871230.170826592782
3.4032-4.28530.1741300.147526622792
4.2853-28.69980.18491550.162227452900
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)
10.003-0.005-0.00150.01030.01170.0104-0.14790.00030.08320.0897-0.1958-0.02140.1580.015500.1015-0.07650.0162-0.2014-0.06830.0373-23.2061-45.690455.3319
20.00140.0067-0.0030.012-0.00450.006-0.0123-0.0129-0.02240.02210.0013-0.00370.00880.0032-00.13390.00940.00040.08010.01630.0734-24.3567-38.460458.9396
30.00490.00130.00180.0049-0.00340.0012-0.01690.0003-0.0241-0.03860.03410.0218-0.0059-0.0399-00.09540.0094-0.00490.09770.00930.0792-28.6234-30.250249.7196
40.0002-0.0025-0.00390.00820.01540.00570.02810.07250.02880.0590.00370.05480.01460.006600.1533-0.08370.0327-0.1749-0.05380.134-26.9236-56.09244.0466
50.022-0.02150.00010.01520.01340.00380.04750.00690.17770.156-0.0377-0.0636-0.00470.0433-00.00930.01490.01060.06070.02420.143-11.0867-17.833942.6238
60.0003-0.0037-0.00430.01160.00610.00450.01180.0190.026-0.04020.0530.0001-0.01020.0953-00.06280.0174-0.00560.11610.00690.0975-13.3124-31.393339.2911
70.0115-0.01330.00570.0065-0.00210.0035-0.0324-0.0060.035-0.0444-0.0309-0.0539-0.0376-0.065700.09430.04170.0090.05090.0230.1759-23.5758-8.218937.2554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 59 )A2 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 92 )A60 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 119 )A93 - 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 160 )B120 - 160

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