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- PDB-1iuq: The 1.55 A Crystal Structure of Glycerol-3-Phosphate Acyltransferase -

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Basic information

Entry
Database: PDB / ID: 1iuq
TitleThe 1.55 A Crystal Structure of Glycerol-3-Phosphate Acyltransferase
ComponentsGlycerol-3-Phosphate Acyltransferase
KeywordsTRANSFERASE / OPEN TWISTED ALPHA/BETA / FOUR HELIX BUNDLE
Function / homology
Function and homology information


: / glycerol-3-phosphate 1-O-acyltransferase / glycerol-3-phosphate O-acyltransferase activity / phosphatidylglycerol biosynthetic process / 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 / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsTamada, T. / Feese, M.D. / Kato, Y. / Kuroki, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Substrate recognition and selectivity of plant glycerol-3-phosphate acyltransferases (GPATs) from Cucurbita moscata and Spinacea oleracea.
Authors: Tamada, T. / Feese, M.D. / Ferri, S.R. / Kato, Y. / Yajima, R. / Toguri, T. / Kuroki, R.
History
DepositionMar 6, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerol-3-Phosphate Acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,19912
Polymers41,1661
Non-polymers1,03311
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.138, 63.604, 115.862
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


Mass: 41165.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucurbita moschata (crookneck pumpkin) / Plasmid: pET-17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P10349, glycerol-3-phosphate 1-O-acyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.6-1.8M AMMONIUM SULFATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMsodium phosphate1droppH8.0
20.5 M1dropNaCl
314 mg/mlprotein1drop
420 mMsodium phosphate1droppH8.0
54-25 %PEG40001reservoir
6100 mMammonium acetate1reservoir
710 %(v/v)2-propanol1reservoir
8100 mMcitrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.548→27.125 Å / Num. all: 61882 / Num. obs: 60415 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 20.27 Å2 / Rsym value: 0.035 / Net I/σ(I): 9.2
Reflection shellResolution: 1.548→1.61 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 5411 / Rsym value: 0.292 / % possible all: 86.6
Reflection
*PLUS
Highest resolution: 1.55 Å / Num. obs: 61882 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Highest resolution: 1.55 Å / % possible obs: 86.6 % / Rmerge(I) obs: 0.292

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.55→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.996 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21906 3127 5.1 %RANDOM
Rwork0.20124 ---
obs0.20216 58534 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.957 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2---1.39 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.55→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 61 390 3247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212910
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.9793940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2933355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.65815529
X-RAY DIFFRACTIONr_chiral_restr0.1190.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022183
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.31532
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5360
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.354
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1221.51788
X-RAY DIFFRACTIONr_mcangle_it2.0522891
X-RAY DIFFRACTIONr_scbond_it3.76631122
X-RAY DIFFRACTIONr_scangle_it5.7834.51049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 196
Rwork0.296 3676
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.862
LS refinement shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.61 Å

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