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- PDB-9g5f: The structure of Aspergillus fumigatus UDP-GlcNAc pyrophosphoryla... -

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Basic information

Entry
Database: PDB / ID: 9g5f
TitleThe structure of Aspergillus fumigatus UDP-GlcNAc pyrophosphorylase in complex with a fragment
Components(UDP-N-acetylglucosamine ...) x 2
KeywordsTRANSFERASE / Aspergillus / UAP1 / fragment
Function / homology
Function and homology information


UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process
Similarity search - Function
UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Chem-GN1 / 4-(2-hydroxyethyl)phenol / UDP-N-acetylglucosamine diphosphorylase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsYan, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
CitationJournal: To Be Published
Title: Exploration of starting points for the chemical validation of UDP-N-acetylglucosamine pyrophosphorylase in Aspergillus fumigatus
Authors: Yan, K. / Stanley, M. / Raimi, O. / Kowalski, B. / Gurvic, D. / Grillenberger, S. / Chen, X. / Ferenbach, A.T. / Dorfmueller, H. / van Aalten, D.M.F.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: UDP-N-acetylglucosamine diphosphorylase
A: UDP-N-acetylglucosamine diphosphorylase
C: UDP-N-acetylglucosamine diphosphorylase
D: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,88714
Polymers215,4074
Non-polymers1,48010
Water17,222956
1
B: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4825
Polymers53,8801
Non-polymers6024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5965
Polymers53,8801
Non-polymers7164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine diphosphorylase


Theoretical massNumber of molelcules
Total (without water)53,8231
Polymers53,8231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9863
Polymers53,8231
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.430, 139.780, 144.190
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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UDP-N-acetylglucosamine ... , 2 types, 4 molecules BACD

#1: Protein UDP-N-acetylglucosamine diphosphorylase


Mass: 53880.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: KXV57_008857 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A229XUD0, UDP-N-acetylglucosamine diphosphorylase
#2: Protein UDP-N-acetylglucosamine diphosphorylase


Mass: 53823.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: KXV57_008857 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A229XUD0, UDP-N-acetylglucosamine diphosphorylase

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-GN1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 964 molecules

#4: Chemical
ChemComp-YRL / 4-(2-hydroxyethyl)phenol / p-tyrosol


Mass: 138.164 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium acetate 25 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.62→52.33 Å / Num. obs: 239403 / % possible obs: 84.7 % / Redundancy: 6.3 % / CC1/2: 1 / Net I/σ(I): 18.7
Reflection shellResolution: 1.62→1.65 Å / Num. unique obs: 4911 / CC1/2: 0.319

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→52.33 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.155 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24652 11944 5 %RANDOM
Rwork0.20924 ---
obs0.21104 227341 84.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.877 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å2-0 Å2-0.57 Å2
2---2.17 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.62→52.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14620 0 100 956 15676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01215162
X-RAY DIFFRACTIONr_bond_other_d0.0030.01614049
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.65220509
X-RAY DIFFRACTIONr_angle_other_deg0.5441.57132872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54951912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.401586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.022102621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.22239
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217189
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022899
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_it3.3763.7517555
X-RAY DIFFRACTIONr_mcbond_other3.3733.757555
X-RAY DIFFRACTIONr_mcangle_it4.4975.6029432
X-RAY DIFFRACTIONr_mcangle_other4.4975.6029433
X-RAY DIFFRACTIONr_scbond_it3.7884.0387607
X-RAY DIFFRACTIONr_scbond_other3.7884.0387608
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.545.91611056
X-RAY DIFFRACTIONr_long_range_B_refined7.10651.75116635
X-RAY DIFFRACTIONr_long_range_B_other7.08950.2916435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 363 -
Rwork0.477 7158 -
obs--36.05 %

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