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- PDB-7u34: The structure of phosphoglucose isomerase from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 7u34
TitleThe structure of phosphoglucose isomerase from Aspergillus fumigatus
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Phosphoglucose isomerase / Aspergillus fumigatus / Antifungal
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative binding / glycolytic process / gluconeogenesis
Similarity search - Function
Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily
Similarity search - Domain/homology
CITRATE ANION / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYan, K. / Kowalski, B. / Fang, W. / van Aalten, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)V001094 United Kingdom
CitationJournal: Mbio / Year: 2022
Title: Phosphoglucose Isomerase Is Important for Aspergillus fumigatus Cell Wall Biogenesis.
Authors: Zhou, Y. / Yan, K. / Qin, Q. / Raimi, O.G. / Du, C. / Wang, B. / Ahamefule, C.S. / Kowalski, B. / Jin, C. / van Aalten, D.M.F. / Fang, W.
History
DepositionFeb 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: 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
A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,48611
Polymers61,8581
Non-polymers62810
Water8,269459
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,97222
Polymers123,7152
Non-polymers1,25620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area15700 Å2
ΔGint-208 kcal/mol
Surface area35500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.452, 84.452, 232.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-996-

HOH

21A-1125-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucose-6-phosphate isomerase


Mass: 61857.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: CDV57_05145 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A229XY52, glucose-6-phosphate isomerase

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Non-polymers , 5 types, 469 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.4 M sodium citrate dihydrate, 0.1 M Hepes-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.56→79.359 Å / Num. obs: 71374 / % possible obs: 95.8 % / Redundancy: 26.4 % / Biso Wilson estimate: 16.81 Å2 / CC1/2: 1 / Net I/σ(I): 19.7
Reflection shellResolution: 1.56→1.745 Å / Num. unique obs: 3567 / CC1/2: 0.795

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Processing

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

7oyl


Resolution: 1.56→58.01 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 3664 5.13 %
Rwork0.1572 67699 -
obs0.1586 71363 59.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.68 Å2 / Biso mean: 22.22 Å2 / Biso min: 6.5 Å2
Refinement stepCycle: final / Resolution: 1.56→58.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 66 459 4831
Biso mean--44.12 28.39 -
Num. residues----557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.581.2610.355332331
1.58-1.60.339250.26911851904
1.6-1.630.3478200.29353663868
1.63-1.650.2179230.2544146410
1.65-1.680.3393340.262551655012
1.68-1.70.2747370.236467270916
1.7-1.730.3102480.228582987719
1.73-1.760.245540.2203970102423
1.76-1.80.2483600.2071166122627
1.8-1.840.2143680.20871356142431
1.84-1.880.25111070.20481628173538
1.88-1.920.2211190.19352005212446
1.92-1.970.20361470.18792333248054
1.97-2.020.1931370.19312720285763
2.02-2.080.22022110.18283616382784
2.08-2.150.21492460.18254297454399
2.15-2.220.2022320.175443854617100
2.22-2.310.21182240.164143544578100
2.31-2.420.18092310.161444034634100
2.42-2.540.19482330.157143814614100
2.54-2.70.19622020.157444264628100
2.7-2.910.18972290.160644384667100
2.91-3.210.17532590.149743934652100
3.21-3.670.17032300.138544974727100
3.67-4.620.13242510.119245114762100
4.62-58.010.17482560.158347795035100

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