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- PDB-1p1i: Crystal structure of the NAD+-bound 1L-myo-inositol 1-phosphate s... -

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Basic information

Entry
Database: PDB / ID: 1p1i
TitleCrystal structure of the NAD+-bound 1L-myo-inositol 1-phosphate synthase
ComponentsInositol-3-phosphate synthase
KeywordsISOMERASE / NAD+ / 1L-myo-inositol 1-phosphate
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
Glyceraldehyde-3-phosphate dehydrogenase-like fold / Glyceraldehyde-3-phosphate dehydrogenase-like domain / 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 ...Glyceraldehyde-3-phosphate dehydrogenase-like fold / Glyceraldehyde-3-phosphate dehydrogenase-like domain / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Inositol-3-phosphate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7424
Polymers119,4162
Non-polymers1,3272
Water2,882160
1
A: Inositol-3-phosphate synthase
B: Inositol-3-phosphate synthase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)241,4858
Polymers238,8314
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area33680 Å2
ΔGint-212 kcal/mol
Surface area71350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.384, 97.344, 122.887
Angle α, β, γ (deg.)90.00, 126.53, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the crystallographic two-fold axis.

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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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.07 Å3/Da / Density % sol: 59.87 %
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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9704 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9704 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 56444 / Num. obs: 55707 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 100
Reflection
*PLUS
Num. measured all: 56444 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.288 4616 random
Rwork0.209 --
all0.234 55707 -
obs0.219 45379 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.456 Å20 Å2-3.627 Å2
2---13.722 Å20 Å2
3---9.266 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7915 0 88 160 8163
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.35
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3nadh.param
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.36

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