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- PDB-1jkf: Holo 1L-myo-inositol-1-phosphate Synthase -

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Basic information

Entry
Database: PDB / ID: 1jkf
TitleHolo 1L-myo-inositol-1-phosphate Synthase
Componentsmyo-inositol-1-phosphate synthase
KeywordsISOMERASE / Rossmann Fold
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 / MAD / Resolution: 2.4 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: Structural Studies of MIP Synthase
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: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / 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)120,7424
Polymers119,4162
Non-polymers1,3272
Water9,692538
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)241,4858
Polymers238,8314
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)151.042, 95.959, 121.291
Angle α, β, γ (deg.)90, 126.04, 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 dimer in the asymmetric unit and a crystallographic 2-fold axis relating the two dimers that make up the tetramer. The assymmetric unit 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-NAD / 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


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 8000, sodium acetate, water, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
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: 0.9794, 0.9796, 0.9464
DetectorDetector: CCD / Date: Mar 28, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.94641
ReflectionResolution: 2.4→500 Å / Num. all: 91546 / Num. obs: 49388 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.85 % / Rsym value: 0.048 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.5 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.338 / % possible all: 92.6
Reflection
*PLUS
Lowest resolution: 500 Å / Num. measured all: 91546 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.338

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→10 Å / σ(F): 2 / Stereochemistry target values: CNS, Terwilliger
RfactorNum. reflection% reflectionSelection details
Rfree0.243 5745 -Random
Rwork0.205 ---
all0.207 106258 --
obs0.246 80871 57.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7347 0 88 538 7973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.927
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shellResolution: 2.4→2.42 Å /
RfactorNum. reflection
Rwork0.268 -
obs-33129
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.207 / Rfactor obs: 0.205 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0095
LS refinement shell
*PLUS
Rfactor Rwork: 0.268

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