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- PDB-6tn3: Crystal Structure of Aspergillus fumigatus UDP-N-acetylglucosamin... -

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Basic information

Entry
Database: PDB / ID: 6tn3
TitleCrystal Structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase in complex with GlcNAc-1P
ComponentsUDP-N-acetylglucosamine pyrophosphorylase
KeywordsTRANSFERASE / Aspergillus fumigatus / anti-fungal / pyrophosphorylase
Function / homology
Function and homology information


sporulation / 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 / 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
Chem-GN1 / PHOSPHATE ION / UDP-N-acetylglucosamine diphosphorylase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.282 Å
AuthorsRaimi, O.G. / Guerrero, R.H.
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
DepositionDec 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_chiral / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_PDB_caveat.text / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_validate_chiral.auth_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 29, 2021Group: Data collection / Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / pdbx_database_proc
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _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_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jan 24, 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: UDP-N-acetylglucosamine pyrophosphorylase
B: UDP-N-acetylglucosamine pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9834
Polymers113,5872
Non-polymers3962
Water4,161231
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)57,1903
Polymers56,7941
Non-polymers3962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.736, 138.140, 145.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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: isolated from a genetically manipulated source
Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
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: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.28→20 Å / Num. obs: 49491 / % possible obs: 95.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 43.69 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 11.2
Reflection shellResolution: 2.28→2.36 Å / Rmerge(I) obs: 0.392 / Num. unique obs: 4051

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YQS

2yqs


Resolution: 2.282→19.925 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.02
RfactorNum. reflection% reflection
Rfree0.2592 2507 5.07 %
Rwork0.2055 --
obs0.2083 49488 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.23 Å2 / Biso mean: 48.6359 Å2 / Biso min: 20.96 Å2
Refinement stepCycle: final / Resolution: 2.282→19.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7113 0 24 231 7368
Biso mean--42.47 44.51 -
Num. residues----905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097292
X-RAY DIFFRACTIONf_angle_d0.9989834
X-RAY DIFFRACTIONf_chiral_restr0.0611074
X-RAY DIFFRACTIONf_plane_restr0.0061277
X-RAY DIFFRACTIONf_dihedral_angle_d16.9964430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2821-2.32590.34531140.2561179267
2.3-2.380.21161580.1819279095
2.3259-2.37330.29051420.2536250495
2.3733-2.42480.321560.2453263397
2.4248-2.48120.34351270.2464256896
2.4812-2.54310.31711560.2578265097
2.5431-2.61170.31621460.2535261897
2.6117-2.68840.34591380.2505261097
2.6884-2.77490.30671350.2397268398
2.7749-2.87380.31331510.2478261798
2.8738-2.98850.32721270.2386267298
2.9885-3.1240.29091180.2415268298
3.124-3.28810.30861240.2354269198
3.2881-3.4930.27051500.2172266198
3.493-3.76110.25991690.1976265198
3.7611-4.13650.21931330.179270898
4.1365-4.72810.18511270.1647270697
4.7281-5.93070.24381360.1758274598

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