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- PDB-7piz: The structure of phosphoglucomutase from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 7piz
TitleThe structure of phosphoglucomutase from Candida albicans
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
Function and homology information
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 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

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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: 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

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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

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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

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