[English] 日本語
Yorodumi
- PDB-6qmf: Phosphopantetheine adenylyltransferase from Mycobacterium tubercu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qmf
TitlePhosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in complex with 5-[3-(1H-indol-3-yl)propoxy]-1-phenyl-1H-pyrazole-4-carboxylic acid at 1.8A resolution.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / CoaD / PPAT / Complex
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / protein hexamerization / coenzyme A biosynthetic process / ATP 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
3-indol-1-ylpropanoic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.771 Å
AuthorsBlaszczyk, M. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: To Be Published
Title: Fragment linking applied to the discovery of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase inhibitors
Authors: Blaszczyk, M. / El Bakali, J. / Boland, J.A. / Spry, C. / Dias, M. / Blundell, T.L. / Abel, C.
History
DepositionFeb 7, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 26, 2020ID: 6G7U
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0603
Polymers17,7921
Non-polymers2672
Water70339
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)108,35818
Polymers106,7546
Non-polymers1,60412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation4_465y-1,x+1,-z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area13340 Å2
ΔGint-93 kcal/mol
Surface area35490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.951, 97.951, 112.729
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-202-

DMS

21A-202-

DMS

31A-312-

HOH

41A-331-

HOH

-
Components

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


Mass: 17792.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: coaD, kdtB, Rv2965c, MTCY349.22, u0002e / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WPA5, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-EQ5 / 3-indol-1-ylpropanoic acid


Mass: 189.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.92 Å3/Da / Density % sol: 57.94 % / Description: cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MPD, CoHexamine Chloride, Cacodylate/Tris / PH range: 6.5-8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.771→67.781 Å / Num. all: 20447 / Num. obs: 20447 / % possible obs: 100 % / Redundancy: 19.5 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.064 / Rsym value: 0.059 / Net I/av σ(I): 5.5 / Net I/σ(I): 27.4 / Num. measured all: 398075
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value
1.771-1.8719.81.4860.529560.3521.5691.486
1.87-1.9820.30.769127970.1790.8070.769
1.98-2.1219.80.361226340.0840.3770.361
2.12-2.2919.90.193.824460.0440.1990.19
2.29-2.520.30.122622620.0280.1280.122
2.5-2.819.50.0798.920580.0190.0840.079
2.8-3.2318.90.0541218300.0140.0590.054
3.23-3.9618.20.04612.915440.0120.050.046
3.96-5.617.80.04214.312140.010.0450.042
5.6-67.78116.40.04411.27060.0120.0490.044

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TFU

1tfu


Resolution: 1.771→67.781 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2206 1046 5.12 %
Rwork0.1917 --
obs0.1931 20446 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.23 Å2 / Biso mean: 47.14 Å2 / Biso min: 21.3 Å2
Refinement stepCycle: final / Resolution: 1.771→67.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 34 39 1231
Biso mean--74.07 42.86 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071195
X-RAY DIFFRACTIONf_angle_d1.1921615
X-RAY DIFFRACTIONf_chiral_restr0.074186
X-RAY DIFFRACTIONf_plane_restr0.005210
X-RAY DIFFRACTIONf_dihedral_angle_d16.653435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7711-1.86450.29571570.271627302887
1.8645-1.98130.25641430.230427502893
1.9813-2.13430.23261610.201627342895
2.1343-2.34910.22661490.18427442893
2.3491-2.6890.26081540.200327632917
2.689-3.38790.22751430.201227932936
3.3879-67.83080.19641390.179128863025
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)
10.1622-0.35520.10581.71420.46060.7710.173-0.3034-0.28610.4199-0.0715-0.94480.12050.31830.40610.3127-0.0206-0.22550.42020.11780.4583-25.945776.836313.9705
20.0990.0073-0.13190.18680.14940.4177-0.2303-0.42990.07870.41840.1403-0.30260.10580.2045-0.07050.22420.0389-0.16950.3753-0.00390.4038-25.725984.232812.2453
30.0755-0.0124-0.05670.04510.02070.0327-0.0691-0.13760.20660.41840.0785-0.2070.06260.0465-00.27550.0201-0.07060.2977-0.05160.2927-34.166691.75696.4935
40.6530.47890.32310.7480.06940.21170.1367-0.1722-0.88590.25270.0667-0.64550.29770.23510.23850.4270.0246-0.17790.33990.22850.4525-36.627765.90816.4823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )A1 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 94 )A59 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 117 )A95 - 117
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 157 )A118 - 157

+
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