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- PDB-1i21: CRYSTAL STRUCTURE OF YEAST GNA1 -

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Basic information

Entry
Database: PDB / ID: 1i21
TitleCRYSTAL STRUCTURE OF YEAST GNA1
ComponentsGLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / ALPHA/BETA / DOMAIN SWAPPING / GNAT
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 / monosaccharide binding / endoplasmic reticulum-Golgi intermediate compartment / Golgi apparatus / endoplasmic reticulum / 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
Glucosamine 6-phosphate N-acetyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 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 5, 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
B: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
M: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
N: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
X: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
Y: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)110,4396
Polymers110,4396
Non-polymers00
Water4,936274
1
A: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
B: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,8132
Polymers36,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-34 kcal/mol
Surface area14020 Å2
MethodPISA
2
M: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
N: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,8132
Polymers36,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34 kcal/mol
Surface area13900 Å2
MethodPISA
3
X: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
Y: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,8132
Polymers36,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-32 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.584, 93.648, 168.311
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-PHOSPHATE N-ACETYLTRANSFERASE / PHOSPHOGLUCOSAMINE TRANSACETYLASE / PHOSPHOGLUCOSAMINE ACETYLASE


Mass: 18406.418 Da / Num. of mol.: 6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
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: ESRF / Beamline: ID14-4 / Wavelength: 0.9324 / Wavelength: 0.9324 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9324 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 37568 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 5.7 / Net I/σ(I): 6.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4.8 / Rsym value: 14.1 / % possible all: 91.5
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 91.6 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1733447.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1886 5 %RANDOM
Rwork0.212 ---
obs0.212 37830 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.17 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--6.74 Å20 Å20 Å2
2--13.61 Å20 Å2
3----6.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7358 0 0 274 7632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.07
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 337 5.6 %
Rwork0.269 5733 -
obs--91.1 %
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
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / Num. reflection Rfree: 1887 / % reflection Rfree: 5 % / Rfactor obs: 0.221 / Rfactor Rfree: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / % reflection Rfree: 5.6 % / Rfactor Rwork: 0.269

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