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- PDB-1i1d: CRYSTAL STRUCTURE OF YEAST GNA1 BOUND TO COA AND GLNAC-6P -

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Basic information

Entry
Database: PDB / ID: 1i1d
TitleCRYSTAL STRUCTURE OF YEAST GNA1 BOUND TO COA AND GLNAC-6P
ComponentsGLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / ALPHA/BETA / DOMAIN SWAPPING / GNAT CONSERVED CORE
Function / homology
Function and homology information


Synthesis of UDP-N-acetyl-glucosamine / glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process / nucleus / cytoplasm
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 / IMIDAZOLE / Glucosamine 6-phosphate N-acetyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPeneff, C. / Mengin-Lecreulx, D. / Bourne, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The crystal structures of Apo and complexed Saccharomyces cerevisiae GNA1 shed light on the catalytic mechanism of an amino-sugar N-acetyltransferase.
Authors: Peneff, C. / Mengin-Lecreulx, D. / Bourne, Y.
History
DepositionFeb 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
B: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
C: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
D: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,77210
Polymers73,2644
Non-polymers2,5086
Water9,764542
1
A: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
D: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0716
Polymers36,6322
Non-polymers1,4394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-33 kcal/mol
Surface area14980 Å2
MethodPISA
2
B: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
C: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7014
Polymers36,6322
Non-polymers1,0692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-27 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.010, 51.619, 91.655
Angle α, β, γ (deg.)90.00, 107.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1027-

HOH

21D-937-

HOH

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Components

#1: Protein
GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE / PHOSPHOGLUCOSAMINE TRANSACETYLASE / PHOSPHOGLUCOSAMINE ACETYLASE


Mass: 18316.074 Da / Num. of mol.: 4 / Mutation: S39C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YFL017C / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (PREP 4)
References: UniProt: P43577, glucosamine-phosphate N-acetyltransferase
#2: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG 600, IMIDAZOLE/MALATE, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117-22 %PEG6001reservoir
20.2 Mimidazole1reservoir
30.4 Mmalate1reservoir
410 mMTris-HCl1drop
5150 mM1dropNaCl
61 mMdithiothreitol1drop
710 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.11
ReflectionResolution: 1.8→30 Å / Num. obs: 62765 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 4.8 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 41.2 / % possible all: 96.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I12

1i12


Resolution: 1.8→24.12 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1131451.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1123 1.8 %RANDOM
Rwork0.183 ---
obs0.183 62747 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.22 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.25 Å2
2--2.46 Å20 Å2
3----2.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 155 542 5713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 173 1.7 %
Rwork0.259 10117 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4LIGAND.PARAMLIGAND.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 1.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15
LS refinement shell
*PLUS
Rfactor Rfree: 0.302 / % reflection Rfree: 1.7 % / Rfactor Rwork: 0.259

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