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- PDB-1rm0: Crystal Structure of Myo-Inositol 1-Phosphate Synthase From Sacch... -

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Basic information

Entry
Database: PDB / ID: 1rm0
TitleCrystal Structure of Myo-Inositol 1-Phosphate Synthase From Saccharomyces cerevisiae In Complex With NAD+ and 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate
Componentsmyo-inositol-phosphate synthase
KeywordsISOMERASE / Myo-Inositol 1-Phosphate Synthase
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
Chem-D6P / : / 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: 2.05 Å
AuthorsJin, X. / Foley, K.M. / Geiger, J.H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The structure of the 1L-myo-inositol-1-phosphate synthase-NAD+-2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate complex demands a revision of the enzyme mechanism.
Authors: Jin, X. / Foley, K.M. / Geiger, J.H.
History
DepositionNov 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,0446
Polymers119,4162
Non-polymers1,6284
Water6,702372
1
A: myo-inositol-phosphate synthase
B: myo-inositol-phosphate synthase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)242,08712
Polymers238,8314
Non-polymers3,2568
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area35060 Å2
ΔGint-222 kcal/mol
Surface area68110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.81, 97.78, 122.29
Angle α, β, γ (deg.)90, 126.3, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein myo-inositol-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)
Gene: INO1 / Production host: Escherichia coli (E. coli)
References: GenBank: 854544, UniProt: P11986*PLUS, inositol-3-phosphate synthase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-D6P / (3,4,5,7-TETRAHYDROXY-HEPT-1-ENYL)-PHOSPHONIC ACID / 2-DEOXY-D-GLUCITOL 6-(E)-VINYLHOMOPHOSPHONATE


Mass: 242.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15O7P
#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.: 372 / 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: 3.14 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 8000, SODIUM ACETATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0093 Å
DetectorType: ADSC QUANTUM 4 / 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: 2.05→35.8 Å / Num. obs: 110431
Reflection shellResolution: 2.05→2.09 Å / % possible all: 98.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→35 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.244 8990 RANDOM
Rwork0.189 --
all0.21 110431 -
obs0.189 89840 -
Refinement stepCycle: LAST / Resolution: 2.05→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8211 0 104 372 8687

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