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- PDB-4miy: Crystal Structure of myo-inositol dehydrogenase from Lactobacillu... -

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Basic information

Entry
Database: PDB / ID: 4miy
TitleCrystal Structure of myo-inositol dehydrogenase from Lactobacillus casei in complex with NAD and myo-inositol
ComponentsInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
KeywordsOXIDOREDUCTASE / NAD / sugar alcohol dehydrogenases / Rossmann fold / dehydrogenase / NAD binding / myo-inositol binding / dehydrogenate
Function / homology
Function and homology information


D-chiro-inositol 1-dehydrogenase / inositol 2-dehydrogenase / inositol 2-dehydrogenase (NAD+) activity / inositol catabolic process / nucleotide binding
Similarity search - Function
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / 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
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase / :
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsBertwistle, D. / Sanders, D.A.R. / Palmer, D.R.J.
CitationJournal: To be Published
Title: Crystal Structure of myo-inositol dehydrogenase from Lactobacillus casei in complex with NAD and myo-inositol
Authors: Bertwistle, D. / Aamudalapalli, H. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionSep 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
B: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
C: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
D: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,63128
Polymers149,0204
Non-polymers4,61124
Water21,4561191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21920 Å2
ΔGint-180 kcal/mol
Surface area48960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.711, 110.624, 127.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase / Myo-inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase


Mass: 37255.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: BL23 / Gene: idh, iolG, iolG1, LCABL_02210 / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: B3W8L3, UniProt: A0A0J9X1Y2*PLUS, inositol 2-dehydrogenase

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Non-polymers , 5 types, 1215 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL / Inositol


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Comment: neurotransmitter, hormone*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1191 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: ammonium sulfate, pH 6.5, MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 6, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.42→83.42 Å / Num. all: 279567 / Num. obs: 279567 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 17.57 Å2 / Rsym value: 0.053 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.42-1.55.50.8020.9219371397200.80297.5
1.5-1.596.10.4751.6234569382050.47598.9
1.59-1.76.50.2912.5232797360780.29199.2
1.7-1.836.80.1744.3229176337450.17499.6
1.83-2.017.10.0997.4220386311430.09999.8
2.01-2.257.30.06410.9205952282980.06499.9
2.25-2.597.40.04813.9184305250650.04899.9
2.59-3.187.30.03816.7155044212540.03899.9
3.18-4.497.10.03714.3118402166180.037100
4.49-48.0586.80.043126416594410.04399.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.94 Å48.06 Å
Translation1.94 Å48.06 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALA3.3.16data scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→48.058 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8554 / SU ML: 0.11 / σ(F): 1.35 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 14113 5.05 %RANDOM
Rwork0.1858 ---
obs0.1871 279440 99.17 %-
all-279567 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.72 Å2 / Biso mean: 20.9064 Å2 / Biso min: 8.74 Å2
Refinement stepCycle: LAST / Resolution: 1.42→48.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10488 0 295 1191 11974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02811068
X-RAY DIFFRACTIONf_angle_d1.48615103
X-RAY DIFFRACTIONf_chiral_restr0.1281776
X-RAY DIFFRACTIONf_plane_restr0.0061926
X-RAY DIFFRACTIONf_dihedral_angle_d14.9184065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.43610.33594400.29518297873794
1.4361-1.4530.29214660.29098633909998
1.453-1.47080.2994690.27178669913898
1.4708-1.48940.28114560.26198735919199
1.4894-1.5090.26824770.25488704918199
1.509-1.52960.26034920.24958689918199
1.5296-1.55150.27314680.24328751921999
1.5515-1.57470.25964740.23398769924399
1.5747-1.59930.24344730.22478747922099
1.5993-1.62550.24544620.22648781924399
1.6255-1.65350.24964420.2228783922599
1.6535-1.68360.23554560.21358836929299
1.6836-1.7160.24395080.20828795930399
1.716-1.7510.23334590.21078830928999
1.751-1.78910.24694400.20748832927299
1.7891-1.83070.23344590.201288729331100
1.8307-1.87650.22844700.201188629332100
1.8765-1.92720.22034390.198788879326100
1.9272-1.98390.22954720.196788799351100
1.9839-2.0480.23854550.196889379392100
2.048-2.12120.21294750.189288789353100
2.1212-2.20610.21324680.188488869354100
2.2061-2.30650.21444610.187589499410100
2.3065-2.42810.21444730.188489249397100
2.4281-2.58020.2034620.186189689430100
2.5802-2.77940.2284640.183989799443100
2.7794-3.05910.21434960.180689669462100
3.0591-3.50160.18315390.163490009539100
3.5016-4.41120.15984880.147491059593100
4.4112-48.08530.16745100.163893849894100

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