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- PDB-1p1f: Crystal structure of apo 1L-myo-inositol 1-phosphate synthase -

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Basic information

Entry
Database: PDB / ID: 1p1f
TitleCrystal structure of apo 1L-myo-inositol 1-phosphate synthase
ComponentsInositol-3-phosphate synthase
KeywordsISOMERASE / apo / enzyme
Function / homology
Function and homology information


Synthesis of IP2, IP, and Ins in the cytosol / inositol-3-phosphate synthase / inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / cytoplasm
Similarity search - Function
Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase, GAPDH-like / Myo-inositol-1-phosphate synthase / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase, GAPDH-like / Myo-inositol-1-phosphate synthase / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Inositol-3-phosphate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsJin, X. / Geiger, J.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structures of NAD(+)- and NADH-bound 1-l-myo-inositol 1-phosphate synthase.
Authors: Jin, X. / Geiger, J.H.
History
DepositionApr 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 18, 2020Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_assembly_prop.biol_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999The differences between the authors' sequence and the database reference sequence are known ...The differences between the authors' sequence and the database reference sequence are known conflicts and have been documented in Swiss Prot entry P11986.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol-3-phosphate synthase
B: Inositol-3-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)119,4162
Polymers119,4162
Non-polymers00
Water2,396133
1
A: Inositol-3-phosphate synthase
B: Inositol-3-phosphate synthase

A: Inositol-3-phosphate synthase
B: Inositol-3-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)238,8314
Polymers238,8314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area28810 Å2
ΔGint-188 kcal/mol
Surface area72350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.543, 97.062, 122.064
Angle α, β, γ (deg.)90.00, 125.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Inositol-3-phosphate synthase / 1L-myo-inositol 1-phosphate synthase / Myo-inositol-1-phosphate synthase / MI-1-P synthase / IPS


Mass: 59707.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P11986, inositol-3-phosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 8000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Details: J., Stein. A., (2000) Acta Crystallogr., Sect.D, 56, 348.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMammonium acetate1drop
310 mMTris1drop
410 mMbeta-mercaptoethanol1drop
52-5 %(v/v)PEG80001reservoir
6100 mMsodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2002 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 44160 / Num. obs: 33338 / % possible obs: 75.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 96.8
Reflection
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.12 / Num. measured all: 44160
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.278 3408 RANDOM
Rwork0.19 --
all0.224 44055 -
obs0.195 33338 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.901 Å20 Å2-4.718 Å2
2---13.513 Å20 Å2
3---8.612 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 0 133 8005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007193
X-RAY DIFFRACTIONc_angle_deg1.39366
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.39

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