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- PDB-6tdf: Crystal structure of Aspergillus fumigatus Glucosamine-6-phosphat... -

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Basic information

Entry
Database: PDB / ID: 6tdf
TitleCrystal structure of Aspergillus fumigatus Glucosamine-6-phosphate N-acetyltransferase 1 in complex with compound 3
ComponentsGlucosamine 6-phosphate N-acetyltransferase
KeywordsTRANSFERASE / fragment screening / anti fungal / Aspergillus fumigatus / inhibitor
Function / homology
Function and homology information


glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process / monosaccharide binding / endoplasmic reticulum-Golgi intermediate compartment / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Glucosamine 6-phosphate N-acetyltransferase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / 6-O-phosphono-alpha-D-glucopyranose / Chem-N3Q / Glucosamine 6-phosphate acetyltransferase, putative
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsRaimi, O.G. / Stanley, M. / Lockhart, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M004139 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Targeting a critical step in fungal hexosamine biosynthesis.
Authors: Lockhart, D.E.A. / Stanley, M. / Raimi, O.G. / Robinson, D.A. / Boldovjakova, D. / Squair, D.R. / Ferenbach, A.T. / Fang, W. / van Aalten, D.M.F.
History
DepositionNov 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosamine 6-phosphate N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5134
Polymers21,1261
Non-polymers1,3873
Water81145
1
A: Glucosamine 6-phosphate N-acetyltransferase
hetero molecules

A: Glucosamine 6-phosphate N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0268
Polymers42,2522
Non-polymers2,7746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9610 Å2
ΔGint-36 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.960, 101.710, 55.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-202-

N3Q

21A-202-

N3Q

31A-202-

N3Q

41A-202-

N3Q

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Components

#1: Protein Glucosamine 6-phosphate N-acetyltransferase


Mass: 21126.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_6G02460 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WCU5, glucosamine-phosphate N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-N3Q / 2-[[3,5-bis(chloranyl)-4-(4~{H}-1,2,4-triazol-3-yl)phenyl]-(2-hydroxyethyl)amino]ethanol


Mass: 317.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14Cl2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1. 10% peg 1000, 10%peg 8000 2. 30% peg1500

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2→58.2 Å / Num. obs: 13064 / % possible obs: 94.6 % / Redundancy: 4 % / CC1/2: 1 / Rsym value: 0.049 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.08 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 13064 / CC1/2: 1 / Rsym value: 0.578

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vez

2vez


Resolution: 2.01→58.2 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.049 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 652 5 %RANDOM
Rwork0.2107 ---
obs0.2133 12493 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.66 Å2 / Biso mean: 43.114 Å2 / Biso min: 29.03 Å2
Baniso -1Baniso -2Baniso -3
1-4.61 Å20 Å20 Å2
2---2.53 Å20 Å2
3----2.08 Å2
Refinement stepCycle: final / Resolution: 2.01→58.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 87 45 1446
Biso mean--48.25 54.03 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131430
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171314
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.7321943
X-RAY DIFFRACTIONr_angle_other_deg1.3291.6393038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9855164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.94121.23373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05815235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0411511
X-RAY DIFFRACTIONr_chiral_restr0.0790.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
LS refinement shellResolution: 2.01→2.08 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.422 64 -
Rwork0.359 861 -
obs--93.43 %

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