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- PDB-1i12: CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GNA1 COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1i12
TitleCRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GNA1 COMPLEXED WITH ACCOA
ComponentsGLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / GNAT / ALPHA/BETA
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
ACETYL COENZYME *A / IMIDAZOLE / Glucosamine 6-phosphate N-acetyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 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
DepositionJan 30, 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)76,41310
Polymers73,0364
Non-polymers3,3766
Water11,331629
1
A: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
C: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2065
Polymers36,5182
Non-polymers1,6883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-32 kcal/mol
Surface area13700 Å2
MethodPISA
2
B: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
D: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2065
Polymers36,5182
Non-polymers1,6883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-33 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.559, 51.842, 92.232
Angle α, β, γ (deg.)90.000, 107.81, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1313-

HOH

21D-1231-

HOH

31D-1300-

HOH

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Components

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


Mass: 18259.021 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 (PREP4)
References: UniProt: P43577, glucosamine-phosphate N-acetyltransferase
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.44 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG 600, IMIDAZOLE, MALATE, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
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: ID14-2 / Wavelength: 0.9326 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 1.3→26.82 Å / Num. all: 166110 / Num. obs: 547136 / % possible obs: 96.1 % / Observed criterion σ(I): 1.9 / Redundancy: 2.05 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.045 / Net I/σ(I): 7.9724
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 15590 / Rsym value: 0.376 / % possible all: 92.3
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 92.3 % / Rmerge(I) obs: 0.376

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.3→24.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2235690.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2955 1.8 %RANDOM
Rwork0.21 ---
obs0.21 163383 94.3 %-
all-163383 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.56 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å2-1.72 Å2
2--3.62 Å20 Å2
3----1.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.3→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 214 629 5842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 453 1.7 %
Rwork0.288 25603 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMLIGAND.TOP
X-RAY DIFFRACTION3LIGAND.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 1.8 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.299 / % reflection Rfree: 1.7 % / Rfactor Rwork: 0.288

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