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- PDB-1k30: Crystal Structure Analysis of Squash (Cucurbita moschata) glycero... -

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Basic information

Entry
Database: PDB / ID: 1k30
TitleCrystal Structure Analysis of Squash (Cucurbita moschata) glycerol-3-phosphate (1)-acyltransferase
Componentsglycerol-3-phosphate acyltransferase
KeywordsTRANSFERASE / Four-helix bundle
Function / homology
Function and homology information


: / glycerol-3-phosphate 1-O-acyltransferase / glycerol-3-phosphate O-acyltransferase activity / : / CDP-diacylglycerol biosynthetic process / chloroplast stroma
Similarity search - Function
Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal / Glycerol-3-phosphate (1)-acyltransferase / Glycerol-3-phosphate (1)-acyltransferase / Glycerol-3-phosphate O-acyltransferase, chloroplast / Glycerol-3-phosphate O-acyltransferase, alpha helical bundle, N-terminal / GPAT, N-terminal domain superfamily / Glycerol-3-phosphate acyltransferase N-terminal / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases ...Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal / Glycerol-3-phosphate (1)-acyltransferase / Glycerol-3-phosphate (1)-acyltransferase / Glycerol-3-phosphate O-acyltransferase, chloroplast / Glycerol-3-phosphate O-acyltransferase, alpha helical bundle, N-terminal / GPAT, N-terminal domain superfamily / Glycerol-3-phosphate acyltransferase N-terminal / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glycerol-3-phosphate acyltransferase ATS12, chloroplastic
Similarity search - Component
Biological speciesCucurbita moschata (crookneck pumpkin)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsTurnbull, A.P. / Rafferty, J.B. / Sedelnikova, S.E. / Slabas, A.R. / Schierer, T.P. / Kroon, J.T. / Simon, J.W. / Fawcett, T. / Nishida, I. / Murata, N. / Rice, D.W.
Citation
Journal: Structure / Year: 2001
Title: Analysis of the structure, substrate specificity, and mechanism of squash glycerol-3-phosphate (1)-acyltransferase.
Authors: Turnbull, A.P. / Rafferty, J.B. / Sedelnikova, S.E. / Slabas, A.R. / Schierer, T.P. / Kroon, J.T. / Simon, J.W. / Fawcett, T. / Nishida, I. / Murata, N. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray analysis of the glycerol-3-phosphate 1-acyltransferase from squash (Cucurbita moschata).
Authors: Turnbull, A.P. / Rafferty, J.B. / Sedelnikova, S.E. / Slabas, A.R. / Schierer, T.P. / Kroon, J.T. / Nishida, I. / Murata, N. / Simon, J.W. / Rice, D.W.
History
DepositionOct 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: glycerol-3-phosphate acyltransferase


Theoretical massNumber of molelcules
Total (without water)40,9691
Polymers40,9691
Non-polymers00
Water8,521473
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.134, 65.098, 103.298
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 glycerol-3-phosphate acyltransferase / glycerol-3-phosphate (1)-acyltransferase / GPAT


Mass: 40968.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucurbita moschata (crookneck pumpkin) / Gene: PLSB / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P10349, glycerol-3-phosphate 1-O-acyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 43.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM citrate buffer, 100mM ammonium acetate, 10%(v/v) 2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114-25 %PEG40001reservoir
2100 mMcitrate1reservoir
3100 mMammonium acetate1reservoir
410 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54182 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 9, 1999 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 1.9→17 Å / Num. all: 32652 / Num. obs: 32652 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2085 / % possible all: 95.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 95.9 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→17 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1612 -random
Rwork0.186 ---
all0.188 30309 --
obs0.188 30309 96.33 %-
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 0 473 3294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.026
X-RAY DIFFRACTIONp_bond_d0.009
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection
Rfree0.291 107
Rwork0.257 -
obs-2007
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 17 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2

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