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- PDB-6g9v: Crystal structure of Aspergillus fumigatus UDP-N-acetylglucosamin... -

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Basic information

Entry
Database: PDB / ID: 6g9v
TitleCrystal structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase(AfUAP1) in complex with UDPGlcNAc, pyrophosphate and Mg2+
ComponentsUDP-N-acetylglucosamine pyrophosphorylase
KeywordsTRANSFERASE / cell wall / anti fungal / pyrophosphorylase / Aspergillus fumigatus
Function / homology
Function and homology information


UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / metal ion binding
Similarity search - Function
UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine diphosphorylase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRaimi, O.G. / Hurtado-Guerrero, R. / Borodin, V. / Urbaniak, M. / Ferguson, M. / van Aalten, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M004139 United Kingdom
CitationJournal: RSC Chem. Biol. / Year: 2020
Title: A mechanism-inspired UDP-N-acetylglucosamine pyrophosphorylase inhibitor
Authors: Raimi, O.G. / Hurtado-Guerrero, R. / Borodkin, V. / Ferenbach, A. / Urbaniak, M.D. / Ferguson, M.A.J. / van Aalten, D.M.F.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _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: UDP-N-acetylglucosamine pyrophosphorylase
B: UDP-N-acetylglucosamine pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3975
Polymers113,5872
Non-polymers8103
Water10,070559
1
A: UDP-N-acetylglucosamine pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)56,7941
Polymers56,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylglucosamine pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6034
Polymers56,7941
Non-polymers8103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.195, 139.839, 144.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-acetylglucosamine pyrophosphorylase


Mass: 56793.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_7G02180 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WAR0, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate and 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 113044 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.568 / Num. unique obs: 11144

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YQS

2yqs


Resolution: 1.75→19.97 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.499 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1137 1 %RANDOM
Rwork0.20701 ---
obs0.20735 111841 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.261 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å2-0 Å2-0 Å2
2---0.95 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.75→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7262 0 49 559 7870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227503
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.97810136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9124.645338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.606151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8471541
X-RAY DIFFRACTIONr_chiral_restr0.0720.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5451.54619
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04227453
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51632884
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5834.52679
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.745→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 63 -
Rwork0.278 7737 -
obs--100 %

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