[English] 日本語
Yorodumi
- PDB-6ccl: Crystal structure of E.coli Phosphopantetheine Adenylyltransferas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ccl
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 1-benzyl-1H-imidazo[4,5-b]pyridine
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE/antibiotic / PPAT CoaD FBDD phosphopantetheine adenylyltransferase Gram-negative antibacterial antibiotic / TRANSFERASE / TRANSFERASE-antibiotic complex
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
1-benzyl-1H-imidazo[4,5-b]pyridine / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.77 Å
AuthorsMamo, M. / Appleton, B.A.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase from Gram-Negative Bacteria.
Authors: Moreau, R.J. / Skepper, C.K. / Appleton, B.A. / Blechschmidt, A. / Balibar, C.J. / Benton, B.M. / Drumm, J.E. / Feng, B.Y. / Geng, M. / Li, C. / Lindvall, M.K. / Lingel, A. / Lu, Y. / Mamo, ...Authors: Moreau, R.J. / Skepper, C.K. / Appleton, B.A. / Blechschmidt, A. / Balibar, C.J. / Benton, B.M. / Drumm, J.E. / Feng, B.Y. / Geng, M. / Li, C. / Lindvall, M.K. / Lingel, A. / Lu, Y. / Mamo, M. / Mergo, W. / Polyakov, V. / Smith, T.M. / Takeoka, K. / Uehara, K. / Wang, L. / Wei, J.R. / Weiss, A.H. / Xie, L. / Xu, W. / Zhang, Q. / de Vicente, J.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,22111
Polymers36,1482
Non-polymers1,0739
Water5,783321
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)111,66233
Polymers108,4436
Non-polymers3,21927
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area21270 Å2
ΔGint-454 kcal/mol
Surface area33880 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)446,648132
Polymers433,77224
Non-polymers12,876108
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_454x-1/2,y+1/2,z-1/21
crystal symmetry operation14_544-x+1/2,-y-1/2,z-1/21
crystal symmetry operation15_555-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_454z-1/2,-x+1/2,-y-1/21
crystal symmetry operation19_555-z+1/2,-x+1/2,y+1/21
crystal symmetry operation20_544-z+1/2,x-1/2,-y-1/21
crystal symmetry operation21_544y+1/2,z-1/2,x-1/21
crystal symmetry operation22_445-y-1/2,z-1/2,-x+1/21
crystal symmetry operation23_555y+1/2,-z+1/2,-x+1/21
crystal symmetry operation24_454-y-1/2,-z+1/2,x-1/21
Buried area76750 Å2
ΔGint-1395 kcal/mol
Surface area143840 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

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


Mass: 18073.846 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-EXG / 1-benzyl-1H-imidazo[4,5-b]pyridine


Mass: 209.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.3 M ammonium sulfate, 0.2 M potassium thiocyanate, 0.2 M potassium bromide

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.77→36.09 Å / Num. obs: 39709 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Net I/σ(I): 16.3 / Num. measured all: 244099
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.77-1.876.20.67157370.8150.2930.733100
5.6-36.0960.022132210.0090.02499.2

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.77→25.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1927 4.85 %RANDOM
Rwork0.164 ---
obs0.166 39696 99.5 %-
Displacement parametersBiso max: 108.48 Å2 / Biso mean: 28.15 Å2 / Biso min: 13.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.77→25.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 66 321 2877
Biso mean--40.07 41.01 -
Num. residues----318
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d932SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes443HARMONIC5
X-RAY DIFFRACTIONt_it2721HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion353SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3630SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2721HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3712HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion16.36
LS refinement shellResolution: 1.77→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2442 126 4.58 %
Rwork0.2062 2625 -
all0.2079 2751 -
obs--95.03 %
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)
11.0380.3906-0.12010.8511-0.52170.5334-0.0081-0.08690.01960.04650.04570.1171-0.0396-0.0848-0.0376-0.0314-0.00330.0004-0.0375-0.0093-0.007720.7649-13.108346.1513
21.4498-0.94422.91041.7260.06761.5417-0.03980.0822-0.0857-0.21860.11190.2355-0.0604-0.0022-0.07210.0661-0.0647-0.0635-0.040.02160.038114.3381-11.642228.4281
32.4170.493-0.61932.3505-0.3230.0315-0.0024-0.00760.27650.05320.09630.4566-0.0143-0.1086-0.0939-0.0280.011-0.0026-0.0567-0.01660.061914.6991-7.353742.3932
41.32160.1209-0.38733.6806-0.95330.8350.0271-0.00710.0650.0251-0.0636-0.0206-0.0956-0.01480.0366-0.0088-0.0093-0.0059-0.0579-0.0044-0.015428.2119-9.039341.6011
52.0297-0.4169-0.78373.70310.08282.20150.01890.1835-0.277-0.0547-0.07330.0615-0.0886-0.08270.0544-0.01830.0247-0.00720.0176-0.01010.000733.9329-17.319634.9094
60.51980.8956-0.28921.5706-0.0580.30020.0650.0668-0.16570.0442-0.036-0.15230.03950.055-0.0290.00230.0085-0.0192-0.0210.0150.022125.9594-20.695643.9808
71.99240.1677-0.92760.52511.09340-0.00870.06280.0273-0.05080.0215-0.0289-0.16830.0849-0.0128-0.0054-0.02810.0035-0.01940.01710.0019.4947-24.49630.3147
82.99030.7289-0.51750.78440.45050.6919-0.03050.0550.4152-0.0091-0.04020.24070.0429-0.27940.0707-0.0528-0.0138-0.0064-0.0075-0.00490.07473.4153-20.763237.7007
91.46921.6932-0.86930-0.61051.7603-0.0042-0.0764-0.0621-0.0008-0.0923-0.0895-0.09980.15980.0965-0.03580.01910.0051-0.01580.0115-0.030542.1382-23.642155.9317
103.1811-1.184-1.10910.8509-0.08772.0931-0.1353-0.2865-0.16430.0348-0.02070.09180.05850.31720.156-0.0632-0.00160.00250.02150.0168-0.043447.1837-23.573255.6381
111.45230.4068-0.40080.2839-0.91962.5491-0.0248-0.1475-0.0950.16040.0494-0.09970.0482-0.0802-0.0246-0.0233-0.03090.0040.09680.0053-0.002840.2424-25.245961.899
123.18170.27060.42791.81950.78672.73140.08580.2753-0.2569-0.14190.18-0.06670.13540.0945-0.2658-0.03260.0112-0.0247-0.06180.0055-0.046332.3757-28.775150.097
131.83471.0887-0.56920.7658-0.68490.42190.09670.2193-0.1319-0.0396-0.0277-0.03710.00550.0321-0.069-0.00980.0106-0.01580.0050.0087-0.03237.9164-22.283646.4662
141.04971.379-1.78351.2157-0.6780.54020.0068-0.0152-0.0690.102-0.04770.10780.07750.03740.04090.01980.0137-0.00010.02530.01710.080355.1318-33.339643.3095
154.3704-0.8065-0.11330.60340.7330.78960.0175-0.4309-0.185-0.0344-0.00910.03120.05030.1157-0.0084-0.08690.01040.00970.00390.0195-0.050560.7152-26.555446.4942
160.0406-0.14260.09240.1913-0.24190-0.0053-0.0162-0.00270.00520.00010.01150.0044-0.00580.00520.0295-0.05040.0498-0.03750.00850.008926.6678-10.268732.0301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|37 }A2 - 37
2X-RAY DIFFRACTION2{ A|38 - A|47 }A38 - 47
3X-RAY DIFFRACTION3{ A|48 - A|73 }A48 - 73
4X-RAY DIFFRACTION4{ A|74 - A|92 }A74 - 92
5X-RAY DIFFRACTION5{ A|93 - A|109 }A93 - 109
6X-RAY DIFFRACTION6{ A|110 - A|128 }A110 - 128
7X-RAY DIFFRACTION7{ A|129 - A|138 }A129 - 138
8X-RAY DIFFRACTION8{ A|139 - A|160 }A139 - 160
9X-RAY DIFFRACTION9{ B|2 - B|15 }B2 - 15
10X-RAY DIFFRACTION10{ B|16 - B|59 }B16 - 59
11X-RAY DIFFRACTION11{ B|60 - B|80 }B60 - 80
12X-RAY DIFFRACTION12{ B|81 - B|109 }B81 - 109
13X-RAY DIFFRACTION13{ B|110 - B|128 }B110 - 128
14X-RAY DIFFRACTION14{ B|129 - B|137 }B129 - 137
15X-RAY DIFFRACTION15{ B|138 - B|159 }B138 - 159
16X-RAY DIFFRACTION16{ A|201 }A201

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more