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- PDB-4bma: structural of Aspergillus fumigatus UDP-N-acetylglucosamine pyrop... -

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Basic information

Entry
Database: PDB / ID: 4bma
Titlestructural of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase
ComponentsUDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
KeywordsTRANSFERASE / UDP-GLCNAC BIOSYNTHESIS PATHWAY
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
UDP-N-acetylglucosamine diphosphorylase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsFang, W. / Raimi, O.G. / HurtadoGuerrero, R. / vanAalten, D.M.F.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Genetic and Structural Validation of Aspergillus Fumigatus Udp-N-Acetylglucosamine Pyrophosphorylase as an Antifungal Target.
Authors: Fang, W. / Du, T. / Raimi, O.G. / Hurtado-Guerrero, R. / Urbaniak, M.D. / Ibrahim, A.F. / Ferguson, M.A. / Jin, C. / Van Aalten, D.M.
History
DepositionMay 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)113,6793
Polymers113,5872
Non-polymers921
Water5,837324
1
A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8862
Polymers56,7941
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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
MethodPISA
Unit cell
Length a, b, c (Å)55.649, 139.744, 144.744
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 (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS
References: UniProt: Q4WAR0, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.35 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.08→40 Å / Num. obs: 69198 / % possible obs: 98.62 % / Observed criterion σ(I): 2.2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.18
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.06 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YQS

2yqs


Resolution: 2.08→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.745 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26467 3453 5.1 %RANDOM
Rwork0.21187 ---
obs0.21455 64787 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20 Å2
2---1.38 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.08→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 6 324 7482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9689892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0565911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04524.606330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17151307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9071540
X-RAY DIFFRACTIONr_chiral_restr0.1350.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215522
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.075→2.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 240 -
Rwork0.269 4399 -
obs--97.93 %

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