[English] 日本語
Yorodumi
- PDB-7pjc: The structure of Candida albicans phosphoglucomutase with isothia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pjc
TitleThe structure of Candida albicans phosphoglucomutase with isothiazolone modification on Cys359
ComponentsPhosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / candida / fungi
Function / homologyAlpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / Chem-A4W
Function and homology information
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsYan, K. / van Aalten, D.M.F.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust200208/Z/15/Z United Kingdom
Medical Research Council (MRC, United Kingdom)V001094 United Kingdom
CitationJournal: To Be Published
Title: Targeting an essential step in the biosynthetic pathway of uridine diphosphate glucose in Aspergillus fumigatus
Authors: Yan, K. / Stanley, M. / Kowalski, B. / Raimi, O.G. / Ferenbach, A.T. / Wei, P. / Yuan, H. / Fang, W. / van Aalten, D.M.F.
History
DepositionAug 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Phosphoglucomutase
A: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,10015
Polymers124,5802
Non-polymers1,52013
Water11,295627
1
B: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1008
Polymers62,2901
Non-polymers8107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0007
Polymers62,2901
Non-polymers7106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.744, 86.444, 110.154
Angle α, β, γ (deg.)90.000, 92.740, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphoglucomutase


Mass: 62290.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gly -4 Expression tag Pro -3 Expression tag Leu -2 Expression tag Gly -1 Restriction site Ser 0 Restriction site
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: PGM2, CAALFM_CR02820WA, orf19.2841 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLys
References: phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical ChemComp-A4W / ~{N}-(3-chloranyl-2-fluoranyl-phenyl)-3-sulfanyl-propanamide


Mass: 233.690 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9ClFNOS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM lithium sulphate monohydrate, 100 mM Tris-HCl pH 8.5, 30% w/v polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.11→67.975 Å / Num. obs: 47519 / % possible obs: 93 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.18 Å2 / CC1/2: 0.993 / Net I/σ(I): 4
Reflection shellResolution: 2.11→2.339 Å / Num. unique obs: 2376 / CC1/2: 0.855

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PIZ

7piz


Resolution: 2.11→67.97 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 2324 4.89 %
Rwork0.1887 45155 -
obs0.192 47479 66.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.32 Å2 / Biso mean: 31.5784 Å2 / Biso min: 9.05 Å2
Refinement stepCycle: final / Resolution: 2.11→67.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8507 0 56 627 9190
Biso mean--69.44 30.6 -
Num. residues----1102
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.160.412460.247468742
2.16-2.20.4642190.26332742937
2.2-2.260.2966280.243454757514
2.26-2.310.3308570.260485591222
2.31-2.370.3209590.24931226128531
2.37-2.440.2832950.24741669176442
2.44-2.520.35961110.25652178228955
2.52-2.610.35681340.27212776291069
2.61-2.720.31581860.26313654384092
2.72-2.840.28591620.25963976413898
2.84-2.990.31441990.24753987418699
2.99-3.180.282040.20923992419699
3.18-3.420.28281650.18014001416699
3.42-3.770.26182080.15653992420099
3.77-4.310.19492180.139539834201100
4.31-5.430.19962420.13173971421399
5.44-67.970.2172310.1724006423798
Refinement TLS params.Method: refined / Origin x: -7.2887 Å / Origin y: -0.193 Å / Origin z: -16.9365 Å
111213212223313233
T0.031 Å2-0.0513 Å20.0351 Å2--0.1553 Å20.1127 Å2--0.0344 Å2
L1.2934 °20.0115 °20.3915 °2-0.4908 °20.2789 °2--1.5274 °2
S-0.106 Å °0.2411 Å °-0.0431 Å °-0.0956 Å °-0.0463 Å °0.0278 Å °-0.1147 Å °0.0065 Å °0.0053 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB5 - 560
2X-RAY DIFFRACTION1allA5 - 560
3X-RAY DIFFRACTION1allA601
4X-RAY DIFFRACTION1allD1 - 10
5X-RAY DIFFRACTION1allS1 - 627

+
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