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- PDB-4ag9: C. elegans glucosamine-6-phosphate N-acetyltransferase (GNA1): te... -

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Basic information

Entry
Database: PDB / ID: 4ag9
TitleC. elegans glucosamine-6-phosphate N-acetyltransferase (GNA1): ternary complex with coenzyme A and GlcNAc
ComponentsGLUCOSAMINE-6-PHOSPHATE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process
Similarity search - Function
Glucosamine 6-phosphate N-acetyltransferase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-16G / COENZYME A / Glucosamine 6-phosphate N-acetyltransferase
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDorfmueller, H.C. / Fang, W. / Rao, F.V. / Blair, D.E. / Attrill, H. / Shepherd, S.M. / van Aalten, D.M.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural and Biochemical Characterization of a Trapped Coenzyme a Adduct of Caenorhabditis Elegans Glucosamine-6-Phosphate N-Acetyltransferase 1.
Authors: Dorfmueller, H.C. / Fang, W. / Rao, F.V. / Blair, D.E. / Attrill, H. / Van Aalten, D.M.F.
History
DepositionJan 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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 / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: GLUCOSAMINE-6-PHOSPHATE N-ACETYLTRANSFERASE
B: GLUCOSAMINE-6-PHOSPHATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2248
Polymers36,9622
Non-polymers2,2626
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-32.8 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.872, 53.353, 135.096
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 GLUCOSAMINE-6-PHOSPHATE N-ACETYLTRANSFERASE / PHOSPHOGLUCOSAMINE ACETYLASE / PHOSPHOGLUCOSAMINE TRANSACETYLASE


Mass: 18481.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUE CYS141 FORMS A DISULPHIDE WITH THE COA. CYS158 FROM THE A AND B CHAINS FORM A DISULPHIDE
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Strain: COSMID B0024
Description: C. ELEGANS COSMID B0024 DNA (SANGER INSTITUTE, CAMBRIDGESHIRE)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q17427, glucosamine-phosphate N-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 5 MM ACCOA, GLCN-6-P, GLCNAC AND 0.1 M TRIS-HYDROCHLORIDE PH 8.5, 0.2 M SODIUM ACETATE TRIHYDRATE AND 30% (V/V) PEG 3350 AND 11 MM BACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 34633 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.5 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AG7

4ag7


Resolution: 1.76→14.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.692 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23216 715 2.1 %RANDOM
Rwork0.19042 ---
obs0.19124 33878 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.76→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 142 411 3133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022774
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2892.0243764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7775326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28824.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28915464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2971516
X-RAY DIFFRACTIONr_chiral_restr0.1410.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212030
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: 1.764→1.809 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 42 -
Rwork0.234 1779 -
obs--74.91 %

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