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- PDB-7oyl: Phosphoglucose isomerase of Aspergillus fumigatus in complexed wi... -

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Basic information

Entry
Database: PDB / ID: 7oyl
TitlePhosphoglucose isomerase of Aspergillus fumigatus in complexed with Glucose-6-phosphate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Fungal pathogen / phosphoglucose isomerase
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative binding / gluconeogenesis / glycolytic process
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
6-O-phosphono-beta-D-glucopyranose / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsRaimi, O.G. / Yan, K. / Fang, W. / van Aalten, D.M.F.
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
DepositionJun 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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
A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,67210
Polymers61,8581
Non-polymers8159
Water8,917495
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,34420
Polymers123,7152
Non-polymers1,62918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area16650 Å2
ΔGint-153 kcal/mol
Surface area35200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.251, 85.251, 232.503
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-1137-

HOH

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Components

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Protein / Sugars , 2 types, 2 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.) Neosartorya fumigata (mold) / Gene: CDV57_05145
Details (production host): modified by a 6His tag prior to the GST
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A0A229XY52, glucose-6-phosphate isomerase
#5: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 503 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.41 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Na-Hepes pH 7.5, 1.4M Tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.78→48.03 Å / Num. obs: 82761 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.4
Reflection shellResolution: 1.78→1.844 Å / Rmerge(I) obs: 1.29 / Num. unique obs: 7939

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
MOLREPphasing
PDB_EXTRACT3.27data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GZD

1gzd


Resolution: 1.78→42.66 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.464 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 4139 5 %RANDOM
Rwork0.1541 ---
obs0.1555 78516 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.4 Å2 / Biso mean: 27.762 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.92 Å2
Refinement stepCycle: final / Resolution: 1.78→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 49 495 4853
Biso mean--52.39 39.34 -
Num. residues----557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134616
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174213
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6436295
X-RAY DIFFRACTIONr_angle_other_deg1.5151.5719820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4465608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04323.727220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92815762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8921515
X-RAY DIFFRACTIONr_chiral_restr0.090.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02957
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 281 -
Rwork0.313 5695 -
all-5976 -
obs--99.24 %

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