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- PDB-1p1h: Crystal structure of the 1L-myo-inositol/NAD+ complex -

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Basic information

Entry
Database: PDB / ID: 1p1h
TitleCrystal structure of the 1L-myo-inositol/NAD+ complex
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 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: 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 999 The 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

Downloads & links

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Assembly

Deposited unit
A: Inositol-3-phosphate synthase
B: Inositol-3-phosphate synthase
C: Inositol-3-phosphate synthase
D: Inositol-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,4858
Polymers238,8314
Non-polymers2,6544
Water27,5451529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32810 Å2
ΔGint-193 kcal/mol
Surface area70670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.794, 185.581, 94.078
Angle α, β, γ (deg.)90.00, 114.77, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer in the asymmetric unit.

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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.: 4
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


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1529 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
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: 14-BM-D / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 203310 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 90.4
Reflection
*PLUS
Num. measured all: 214444 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.249 16625 random
Rwork0.208 --
all0.221 --
obs0.212 166393 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.265 Å20 Å2-6.32 Å2
2--0.88 Å20 Å2
3----3.145 Å2
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15784 0 176 1529 17489
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.25
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_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.26

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