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- PDB-1p1k: Crystal structure of the 1L-myo-inositol 1-phosphate synthase com... -

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Basic information

Entry
Database: PDB / ID: 1p1k
TitleCrystal structure of the 1L-myo-inositol 1-phosphate synthase complexed with NADH in the presence of EDTA
ComponentsInositol-3-phosphate synthase
KeywordsISOMERASE / 1L-myo-inositol 1-phosphate / NADH / EDTA / 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
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Inositol-3-phosphate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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

Downloads & links

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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)120,7464
Polymers119,4162
Non-polymers1,3312
Water3,207178
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)241,4938
Polymers238,8314
Non-polymers2,6624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area33670 Å2
ΔGint-218 kcal/mol
Surface area69480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.978, 97.613, 121.717
Angle α, β, γ (deg.)90.00, 126.15, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -x, y, -z

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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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


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


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 8000, EDTA, 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: 1.0093 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 82661 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 99.6
Reflection
*PLUS
% possible obs: 99.8 % / Num. measured all: 161339 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.261 6970 random
Rwork0.209 --
all0.227 82946 -
obs0.213 69073 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.639 Å20 Å2-0.888 Å2
2---8.461 Å20 Å2
3---4.823 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8184 0 88 178 8450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.3
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

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