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- PDB-1la2: Structural analysis of Saccharomyces cerevisiae myo-inositol phos... -

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Basic information

Entry
Database: PDB / ID: 1la2
TitleStructural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase
ComponentsMyo-inositol-1-phosphate synthase
KeywordsISOMERASE / structural genomics / inositol / metabolism / yeast / ino1 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Inositol-3-phosphate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsKniewel, R. / Buglino, J.A. / Shen, V. / Chadna, T. / Beckwith, A. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2002
Title: Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase
Authors: Kniewel, R. / Buglino, J.A. / Shen, V. / Chadna, T. / Beckwith, A. / Lima, C.D.
History
DepositionMar 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE AUTHORS USED SWISSPROT ENTRY P11986. SEVERAL RESIDUES WERE MIS-SEQUENCED IN REFERENCE ...SEQUENCE THE AUTHORS USED SWISSPROT ENTRY P11986. SEVERAL RESIDUES WERE MIS-SEQUENCED IN REFERENCE 1 OF THE SWS ENTRY, AND ARE CORRECTED IN REFERENCE 3 IN THE FEATURES SECTION.

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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
C: Myo-inositol-1-phosphate synthase
D: Myo-inositol-1-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,3618
Polymers240,7074
Non-polymers2,6544
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34010 Å2
ΔGint-202 kcal/mol
Surface area72590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.693, 187.346, 98.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Myo-inositol-1-phosphate synthase / MI-1-P synthase / IPS


Mass: 60176.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: INO1 / Plasmid: pSMT3 (modified pET28b) / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3) / 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.: 692 / 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 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 7% PEG 4000, 0.1M sodium acetate, 5% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16.4 mg/mlprotein1drop
210 mMTris-HCl1droppH8.
350 mM1dropNaCl
41 mMdithiothreitol1drop
57 %PEG40001reservoir
60.1 Msodium acetate1reservoirpH4.6
75 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 11, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. all: 183241 / Num. obs: 180676 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.9
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.3 / % possible all: 91
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 1002153
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS0.9refinement
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3455046.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 4213 5 %RANDOM
Rwork0.224 ---
all-84499 --
obs-83992 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.2485 Å2 / ksol: 0.336188 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å20 Å20 Å2
2--0.81 Å20 Å2
3---2.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16172 0 176 692 17040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 694 5.1 %
Rwork0.307 13036 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5NAD.PARNAD.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.224 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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