[English] 日本語
Yorodumi
- PDB-7piz: The structure of phosphoglucomutase from Candida albicans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7piz
TitleThe structure of phosphoglucomutase from Candida albicans
ComponentsPhosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / candida / fungi
Biological speciesCandida albicans P75010 (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Phosphoglucomutase
B: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0607
Polymers124,5802
Non-polymers4805
Water25,7251428
1
C: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3862
Polymers62,2901
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6745
Polymers62,2901
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.950, 86.841, 109.920
Angle α, β, γ (deg.)90.000, 92.800, 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 P75010 (yeast) / Strain: P75010 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1428 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 291.15 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→25.71 Å / Num. obs: 65230 / % possible obs: 95.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.15 Å2 / CC1/2: 0.979 / Net I/σ(I): 4.5
Reflection shellResolution: 2.15→2.2 Å / Num. unique obs: 4312 / CC1/2: 0.82

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A homology model based on the orthologue protein from human (PDB 5EPC))

5epc


Resolution: 2.15→25.71 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 3207 4.92 %
Rwork0.1955 61984 -
obs0.1986 65191 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.01 Å2 / Biso mean: 21.2341 Å2 / Biso min: 3.65 Å2
Refinement stepCycle: final / Resolution: 2.15→25.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8499 0 25 1428 9952
Biso mean--41.65 27.06 -
Num. residues----1098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.180.31531500.22372646279694
2.18-2.220.27721520.2292646279894
2.22-2.250.31991260.24572645277194
2.25-2.290.30691370.24992681281895
2.29-2.330.28621290.23042671280095
2.33-2.380.31891460.21392680282695
2.38-2.430.26781340.21112658279295
2.43-2.480.27161460.21552700284695
2.48-2.540.30691360.20482689282595
2.54-2.60.28561380.21122641277994
2.6-2.670.291560.19932662281894
2.67-2.750.28561340.20812627276193
2.75-2.840.25961460.2132577272393
2.84-2.940.33911280.21612637276593
2.94-3.060.33991480.23372674282294
3.06-3.190.27421300.20022679280995
3.19-3.360.20791520.17972683283596
3.36-3.570.25611380.18462753289197
3.57-3.850.20491270.17472762288997
3.85-4.230.22451190.17022812293197
4.23-4.840.22621170.15572806292397
4.84-6.090.2121930.17062778297198
6.09-25.710.2121250.17862877300298

+
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://pdbjlvh1.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