[English] 日本語
Yorodumi
- PDB-5o0h: Crystal structure of Phosphopantetheine adenylyltransferase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o0h
TitleCrystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 2-(4-Chloro-3-nitrobenzoyl)benzoic acid (Fragment 6)
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Coenzyme A Biosynthesis
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / 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
Chem-9FN / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsThomas, S.E. / Kim, S.Y. / Mendes, V. / Blaszczyk, M. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cystic Fibrosis Trust United Kingdom
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew.
Authors: Thomas, S.E. / Mendes, V. / Kim, S.Y. / Malhotra, S. / Ochoa-Montano, B. / Blaszczyk, M. / Blundell, T.L.
History
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.title
Revision 1.3Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 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
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0425
Polymers52,4313
Non-polymers6112
Water5,765320
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,08410
Polymers104,8616
Non-polymers1,2234
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14340 Å2
ΔGint-106 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.131, 125.562, 120.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21C-334-

HOH

-
Components

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


Mass: 17476.887 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Gene: coaD, MAB_3259c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-9FN / 2-(4-chloranyl-3-nitro-phenyl)carbonylbenzoic acid


Mass: 305.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8ClNO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200mM Sodium bromide 20-25% PEG 3350 0.1M Bis-Tris propane
PH range: 6.5 to 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.6→65.1 Å / Num. obs: 75801 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 18.61 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.046 / Rrim(I) all: 0.142 / Net I/σ(I): 12.7 / Num. measured all: 730047 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.699.91.223108430109590.6440.4031.2892.499.8
5.06-65.18.90.082294225920.9960.0280.08529.2100

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.26data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O06

5o06


Resolution: 1.599→44.149 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 3665 4.9 %
Rwork0.2216 71114 -
obs0.2232 74779 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.67 Å2 / Biso mean: 25.7503 Å2 / Biso min: 7.56 Å2
Refinement stepCycle: final / Resolution: 1.599→44.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 42 320 3879
Biso mean--40.63 31.49 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083747
X-RAY DIFFRACTIONf_angle_d1.0875114
X-RAY DIFFRACTIONf_chiral_restr0.045600
X-RAY DIFFRACTIONf_plane_restr0.005672
X-RAY DIFFRACTIONf_dihedral_angle_d13.6591381
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5994-1.62040.32681380.317427262864100
1.6204-1.64260.34831380.298827612899100
1.6426-1.66610.31611320.286527492881100
1.6661-1.6910.34281480.285527552903100
1.691-1.71740.30551450.265627542899100
1.7174-1.74560.28391430.25727382881100
1.7456-1.77570.30031370.264927482885100
1.7757-1.8080.24141780.249827402918100
1.808-1.84270.3321520.289127412893100
1.8427-1.88030.33951440.312327522896100
1.8803-1.92120.6141050.46992331243684
1.9212-1.96590.32851260.27412477260390
1.9659-2.01510.24561200.212827882908100
2.0151-2.06960.22441350.227992934100
2.0696-2.13050.24181340.203527652899100
2.1305-2.19920.24961650.202827402905100
2.1992-2.27780.26031140.27262548266291
2.2778-2.3690.24131050.209728402945100
2.369-2.47680.23521700.196227192889100
2.4768-2.60740.23571370.206828292966100
2.6074-2.77070.24051390.208127822921100
2.7707-2.98460.24111450.21227972942100
2.9846-3.28490.2561300.203428342964100
3.2849-3.760.20041630.19632590275393
3.76-4.73630.22251570.172628573014100
4.7363-44.16540.22651650.193129543119100

+
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