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- PDB-4bju: Genetic and structural validation of Aspergillus fumigatus N- ace... -

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Basic information

Entry
Database: PDB / ID: 4bju
TitleGenetic and structural validation of Aspergillus fumigatus N- acetylphosphoglucosamine mutase as an antifungal target
ComponentsN-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE
KeywordsISOMERASE / UDP-GLCNAC BIOSYNTHESIS PATHWAY
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 AMG1, domain III / Phosphoacetylglucosamine mutase AMG1, domain II / 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 ...: / : / Phosphoacetylglucosamine mutase AMG1, domain III / Phosphoacetylglucosamine mutase AMG1, domain II / 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
Phosphoacetylglucosamine mutase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFang, W. / Raimi, O.G. / Hurtado Guerrero, R. / van Aalten, D.M.F.
CitationJournal: Biosci.Rep / Year: 2013
Title: Genetic and Structural Validation of Aspergillus Fumigatus N-Acetylphosphoglucosamine Mutase as an Antifungal Target.
Authors: Fang, W. / Du, T. / Raimi, O.G. / Hurtado Guerrero, R. / Marino, K. / Ibrahim, A.F.M. / Albarbarawi, O. / Ferguson, M.A.J. / Jin, C. / Van Aalten, D.M.F.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 25, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _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: N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE
B: N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0664
Polymers120,0182
Non-polymers492
Water63135
1
A: N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0332
Polymers60,0091
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0332
Polymers60,0091
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.700, 86.570, 185.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.029055, 0.999578, 0.000472), (0.994123, -0.028847, -0.104346), (-0.104288, 0.003501, -0.994541)50.65101, -48.71001, 54.7558

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Components

#1: Protein N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE / N-ACETYLPHOSPHOGLUCOSAMINE MUTASE


Mass: 60008.930 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): PLYSS
References: UniProt: B0XPI4, phosphoacetylglucosamine mutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.5 Å3/Da / Density % sol: 50.75 % / Description: NONE
Crystal growpH: 7.25 / Details: pH 7.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 2.35
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.35 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 50913 / % possible obs: 99.8 % / Observed criterion σ(I): 1.8 / Redundancy: 3.5 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.7
Reflection shellHighest resolution: 2.35 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DKA

2dka


Resolution: 2.35→24.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 18.996 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27691 1048 2.1 %RANDOM
Rwork0.21849 ---
obs0.21965 49799 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.228 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2--1.23 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.35→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8351 0 2 35 8388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198491
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.97111505
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04251088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07524.169367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.848151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4051560
X-RAY DIFFRACTIONr_chiral_restr0.0920.21315
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216374
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: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 55 -
Rwork0.291 3632 -
obs--99.97 %

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