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

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Basic information

Entry
Database: PDB / ID: 5oaw
TitleCrystal structure of Aspergillus fumigatus N-acetylphosphoglucosamine mutase in complex with GlcNAc-6P and magnesium
ComponentsPhosphoacetylglucosamine mutase
KeywordsISOMERASE / 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-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
Similarity search - Domain/homology
Chem-16G / Phosphoacetylglucosamine mutase
Similarity search - Component
Biological speciesAspergillus lentulus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.34 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 24, 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_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoacetylglucosamine mutase
B: Phosphoacetylglucosamine mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9218
Polymers120,0182
Non-polymers9036
Water5,459303
1
A: Phosphoacetylglucosamine mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4274
Polymers60,0091
Non-polymers4183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoacetylglucosamine mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4944
Polymers60,0091
Non-polymers4853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.314, 84.815, 186.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B37 - 538
2114A37 - 538
1214B26 - 540
2214A26 - 540

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.072329, 0.995918, -0.054006), (0.996601, -0.074306, -0.035553), (-0.039421, -0.051251, -0.997908)13.85307, -13.03787, 48.25947

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Components

#1: Protein Phosphoacetylglucosamine mutase / PAGM / Acetylglucosamine phosphomutase / N-acetylglucosamine-phosphate mutase


Mass: 60008.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Serine is phosphorylated / Source: (gene. exp.) Aspergillus lentulus (mold) / Gene: ALT_8497 / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLysS
References: UniProt: A0A0S7E9S6, phosphoacetylglucosamine mutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / N-acetyl-6-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 1000, 100 mM HEPES, pH 7.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.34→20 Å / Num. obs: 48393 / % possible obs: 99.8 % / Redundancy: 3.5 % / Net I/σ(I): 34.7
Reflection shellResolution: 2.35→2.43 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.34→93.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.002 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27753 485 1 %RANDOM
Rwork0.21023 ---
obs0.21092 47852 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.666 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--3.82 Å20 Å2
3----3.45 Å2
Refinement stepCycle: 1 / Resolution: 2.34→93.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7791 0 57 303 8151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.97410808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33551022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2924.006332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.584151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0571555
X-RAY DIFFRACTIONr_chiral_restr0.1010.21265
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215935
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_it2.7485.1444121
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2547.6915129
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2975.3453849
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.5370.7212161
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 7220 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.460.5
Bmedium thermal4.62
LS refinement shellResolution: 2.335→2.396 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 32 -
Rwork0.314 3239 -
obs--92.17 %

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