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- PDB-1jki: myo-Inositol-1-phosphate Synthase Complexed with an Inhibitor, 2-... -

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Basic information

Entry
Database: PDB / ID: 1jki
Titlemyo-Inositol-1-phosphate Synthase Complexed with an Inhibitor, 2-deoxy-glucitol-6-phosphate
Componentsmyo-inositol-1-phosphate synthase
KeywordsISOMERASE / Rossmann fold / inhibitor-bound structure
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
2-DEOXY-GLUCITOL-6-PHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / AMMONIUM ION / Inositol-3-phosphate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStein, A.J. / Geiger, J.H.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The crystal structure and mechanism of 1-L-myo-inositol- 1-phosphate synthase
Authors: Stein, A.J. / Geiger, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: MIP Synthase Structural Studies
Authors: Stein, A.J. / Geiger, J.H.
History
DepositionJul 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: myo-inositol-1-phosphate synthase
B: myo-inositol-1-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,2758
Polymers119,4162
Non-polymers1,8596
Water11,133618
1
A: myo-inositol-1-phosphate synthase
B: myo-inositol-1-phosphate synthase
hetero molecules

A: myo-inositol-1-phosphate synthase
B: myo-inositol-1-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,55016
Polymers238,8314
Non-polymers3,71912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area36200 Å2
ΔGint-228 kcal/mol
Surface area70620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.728, 98.309, 121.855
Angle α, β, γ (deg.)90, 126.093, 90
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer . The tetramer has 222 symmetry with a non-crystallographic 2-fold axis relating the two monomers in the assymmetric unit and a crystallographic 2-fold axis relating the two dimers that make up the tetramer. The operations are x, y, z and -x, y, -z.

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Components

#1: Protein myo-inositol-1-phosphate synthase


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-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-DG6 / 2-DEOXY-GLUCITOL-6-PHOSPHATE


Mass: 246.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O8P
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 60.24 %
Crystal growTemperature: 298 K / Method: co-crystalliztion / pH: 4.5
Details: PEG 8000, sodium acetate, NAD, and 2-deoxy-glucitol-6-phosphate, pH 4.5, co-crystalliztion, temperature 298K
Crystal grow
*PLUS
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: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: SBC / Detector: CCD / Date: Mar 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 92832 / Num. obs: 76517 / % possible obs: 89.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.082 / Net I/σ(I): 13.9
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.304 / % possible all: 89.2
Reflection
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.304

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MIP synthase, PDB 1JKF

1jkf


Resolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: CNS, Terwilliger
RfactorNum. reflection% reflectionSelection details
Rfree0.28 5815 -Random
Rwork0.208 ---
all0.285 73086 --
obs0.214 64050 87.6 %-
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8268 0 120 618 9006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.758
X-RAY DIFFRACTIONc_bond_d0.0099
LS refinement shellResolution: 2.2→2.3 Å /
RfactorNum. reflection
Rfree0.365 98
Rwork0.269 -
obs-822
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.285 / Rfactor obs: 0.208 / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / Rfactor Rwork: 0.269

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