[English] 日本語
Yorodumi
- PDB-6z0q: Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z0q
TitleCrystal structure of SAICAR Synthetase (PurC) from Mycobacterium abscessus in complex with fragment 2
ComponentsPhosphoribosylaminoimidazole-succinocarboxamide synthase
KeywordsLIGASE / SAICAR synthetase / Phosphoribosylaminoimidazole-succinocarboxamide synthase / PurC / Purine Biosynthesis
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase
Similarity search - Domain/homology
Chem-Q4K / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesMycobacteroides abscessus ATCC 19977 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.535 Å
AuthorsThomas, S.E. / Charoensutthivarakul, S. / Coyne, A.G. / Abell, C. / Blundell, T.L.
Funding support Switzerland, United Kingdom, 2items
OrganizationGrant numberCountry
Other privateFondation Botnar Grant No.6063 Switzerland
Other privateCystic Fibrosis Trust SRC010 United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Development of Inhibitors of SAICAR Synthetase (PurC) from Mycobacterium abscessus Using a Fragment-Based Approach.
Authors: Charoensutthivarakul, S. / Thomas, S.E. / Curran, A. / Brown, K.P. / Belardinelli, J.M. / Whitehouse, A.J. / Acebron-Garcia-de-Eulate, M. / Sangan, J. / Gramani, S.G. / Jackson, M. / Mendes, ...Authors: Charoensutthivarakul, S. / Thomas, S.E. / Curran, A. / Brown, K.P. / Belardinelli, J.M. / Whitehouse, A.J. / Acebron-Garcia-de-Eulate, M. / Sangan, J. / Gramani, S.G. / Jackson, M. / Mendes, V. / Floto, R.A. / Blundell, T.L. / Coyne, A.G. / Abell, C.
History
DepositionMay 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2883
Polymers33,9001
Non-polymers3882
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.247, 65.201, 49.051
Angle α, β, γ (deg.)90.000, 110.730, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase


Mass: 33900.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus ATCC 19977 (bacteria)
Gene: purC, MAB_0689 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MHW4, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Chemical ChemComp-Q4K / ethyl (2~{S},3~{R})-3-(5-bromanylpyridin-2-yl)-2-fluoranyl-3-oxidanyl-propanoate


Mass: 292.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11BrFNO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiSO4, 0.1 M Bis-Tris pH 6.0, 22 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.535→65.2 Å / Num. obs: 41377 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.032 / Rrim(I) all: 0.06 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.54-1.623.60.5652139159580.8210.3460.6632.396.6
4.86-65.23.20.028438813560.9980.0180.03439.297.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.21 Å45.88 Å
Translation6.21 Å45.88 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.5.6phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YVQ

6yvq


Resolution: 1.535→45.875 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 2063 4.99 %
Rwork0.1869 39283 -
obs0.1891 41346 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52 Å2 / Biso mean: 23.0403 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 1.535→45.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 21 299 2576
Biso mean--35.38 31.4 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082355
X-RAY DIFFRACTIONf_angle_d1.0293226
X-RAY DIFFRACTIONf_chiral_restr0.047361
X-RAY DIFFRACTIONf_plane_restr0.006427
X-RAY DIFFRACTIONf_dihedral_angle_d11.339842
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5354-1.57110.25861310.2488258396
1.5711-1.61040.31921310.2333257396
1.6104-1.6540.25271100.2275261897
1.654-1.70260.24531550.2132257397
1.7026-1.75760.27561580.2076258897
1.7576-1.82040.23221290.2028261497
1.8204-1.89330.24041400.1914260797
1.8933-1.97950.2471300.1858263197
1.9795-2.08380.22541270.1809261797
2.0838-2.21440.21711250.1839265698
2.2144-2.38530.26291430.1844263698
2.3853-2.62540.26751510.2036263298
2.6254-3.00520.25211370.2039264498
3.0052-3.7860.21521600.1759262998
3.786-45.8750.18711360.1624268297

+
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