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- PDB-7pjc: The structure of Candida albicans phosphoglucomutase with isothia... -

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Basic information

Entry
Database: PDB / ID: 7pjc
TitleThe structure of Candida albicans phosphoglucomutase with isothiazolone modification on Cys359
ComponentsPhosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase / candida / fungi
Function / homologyChem-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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