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- PDB-9g63: The structure of Aspergillus fumigatus UDP-GlcNAc pyrophosphoryla... -

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Basic information

Entry
Database: PDB / ID: 9g63
TitleThe structure of Aspergillus fumigatus UDP-GlcNAc pyrophosphorylase in complex with fragments
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 / UDP-N-acetylglucosamine diphosphorylase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7488
Polymers107,7032
Non-polymers1,0456
Water3,153175
1
B: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9257
Polymers53,8801
Non-polymers1,0456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 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
Unit cell
Length a, b, c (Å)55.493, 136.840, 143.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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UDP-N-acetylglucosamine ... , 2 types, 2 molecules BA

#1: Protein UDP-N-acetylglucosamine diphosphorylase


Mass: 53880.246 Da / Num. of mol.: 1
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.: 1
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, 1 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.: 1 / Source method: obtained synthetically / Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 180 molecules

#4: Chemical ChemComp-A1IHU / 4-bromanyl-2-methyl-pyrazol-3-amine


Mass: 176.015 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6BrN3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1IIR / furan-2-yl(piperazin-1-yl)methanone


Mass: 180.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
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: 2.03→63.39 Å / Num. obs: 71521 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.993 / Net I/σ(I): 6.4
Reflection shellResolution: 2.03→2.06 Å / Num. unique obs: 3455 / CC1/2: 0.297

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→63.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.012 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26353 1905 2.7 %RANDOM
Rwork0.21349 ---
obs0.21489 69490 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.854 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å2-0 Å2-0 Å2
2---2.55 Å2-0 Å2
3---0.61 Å2
Refinement stepCycle: 1 / Resolution: 2.03→63.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 57 175 7462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127468
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166903
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.65510097
X-RAY DIFFRACTIONr_angle_other_deg0.5811.57216126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3225933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.083543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.449101273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021435
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_it3.9144.6013726
X-RAY DIFFRACTIONr_mcbond_other3.9114.6013726
X-RAY DIFFRACTIONr_mcangle_it5.5886.8834646
X-RAY DIFFRACTIONr_mcangle_other5.5876.8844647
X-RAY DIFFRACTIONr_scbond_it4.6614.93742
X-RAY DIFFRACTIONr_scbond_other4.664.9023743
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7987.1925447
X-RAY DIFFRACTIONr_long_range_B_refined8.856.9128102
X-RAY DIFFRACTIONr_long_range_B_other8.80456.9228081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.08 Å
RfactorNum. reflection% reflection
Rfree0.389 161 -
Rwork0.398 4953 -
obs--97.74 %

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