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- PDB-5o9x: Crystal structure of Aspergillus fumigatus N-acetylphosphoglucosa... -

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Basic information

Entry
Database: PDB / ID: 5o9x
TitleCrystal structure of Aspergillus fumigatus N-acetylphosphoglucosamine mutate S69A in complex with glucose1,6bisphosphate
ComponentsPhosphoacetylglucosamine mutase
KeywordsTRANSFERASE / Mutase / N-acetylphosphoglucosamine / Aspergillus fumigatus
Function / homology
Function and homology information


phosphoacetylglucosamine mutase / phosphoacetylglucosamine mutase activity / UDP-N-acetylglucosamine biosynthetic process / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Phosphoacetylglucosamine mutase / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III ...Phosphoacetylglucosamine mutase / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-alpha-D-glucopyranose / Phosphoacetylglucosamine mutase
Similarity search - Component
Biological speciesAspergillus lentulus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsRaimi, O.G. / Hurtado-Guerrero, R.
CitationJournal: Biochem. J. / Year: 2018
Title: Evidence for substrate-assisted catalysis inN-acetylphosphoglucosamine mutase.
Authors: Raimi, O.G. / Hurtado-Guerrero, R. / van Aalten, D.M.F.
History
DepositionJun 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoacetylglucosamine mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5076
Polymers59,9131
Non-polymers5945
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-28 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.860, 87.574, 91.867
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 Phosphoacetylglucosamine mutase / / PAGM / Acetylglucosamine phosphomutase / N-acetylglucosamine-phosphate mutase


Mass: 59912.953 Da / Num. of mol.: 1 / Mutation: S69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus lentulus (mold) / Gene: ALT_8497 / Plasmid: pGEX-6P / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PlysS
References: UniProt: A0A0S7E9S6, phosphoacetylglucosamine mutase
#2: Sugar ChemComp-G16 / 1,6-di-O-phosphono-alpha-D-glucopyranose / Glucose 1,6-bisphosphate


Type: D-saccharide / Mass: 339.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O12P2
IdentifierTypeProgram
a-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1. 0.2 M sodium thiocyanate, 20% PEG 3350 and 0.1 M sodium bromide 2. 0.10 M glycine, 22% PEG 3350 and 0.2 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 51704 / % possible obs: 97.6 % / Redundancy: 3.7 % / Net I/σ(I): 19.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Num. unique obs: 4939 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.997 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20123 519 1 %RANDOM
Rwork0.1649 ---
obs0.1653 50268 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.934 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---0.03 Å20 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 34 471 4649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194253
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.9775762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4295542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29624.076184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53215727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5291531
X-RAY DIFFRACTIONr_chiral_restr0.160.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213174
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_it2.482.3982165
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3923.5792705
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1812.8082088
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.98434.2486786
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 27 -
Rwork0.218 3529 -
obs--94.2 %

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