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- PDB-3nt2: Crystal structure of myo-inositol dehydrogenase from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 3nt2
TitleCrystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor
ComponentsInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
KeywordsOXIDOREDUCTASE / BSIDH / N-terminal Rossmann fold domain / glyceraldehyde-3-phosphate like C-terminal domain / NAD / myo-inositol
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 ...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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3003 Å
AuthorsVan Straaten, K.E. / Palmer, D.R.J. / Sanders, D.A.R.
CitationJournal: Biochem.J. / Year: 2010
Title: Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification.
Authors: van Straaten, K.E. / Zheng, H. / Palmer, D.R. / Sanders, D.A.
History
DepositionJul 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
B: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1184
Polymers76,7892
Non-polymers1,3292
Water2,234124
1
A: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
B: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules

A: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
B: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,2368
Polymers153,5784
Non-polymers2,6584
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area16720 Å2
ΔGint-70 kcal/mol
Surface area51230 Å2
MethodPISA
2
A: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
B: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules

A: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
B: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules

A: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
B: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,35412
Polymers230,3676
Non-polymers3,9876
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16740 Å2
ΔGint-95 kcal/mol
Surface area85190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.368, 184.368, 184.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

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


Mass: 38394.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU39700, E83G, idh, iolG, NP_391849.2 / Plasmid: PHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: P26935, inositol 2-dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.4
Details: 0.1M tri-sodium citrate pH 5.4, 2.6M ammonium sulfate, microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 21, 2009
RadiationMonochromator: SAGITALLY FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→22.04 Å / Num. obs: 45289 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.18 % / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Χ2: 0.96 / Net I/σ(I): 9.5 / Scaling rejects: 3827
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.3-2.388.010.7391.73689546021.01100
2.38-2.4810.890.6862.14959145481.01100
2.48-2.5911.920.6192.55438945551100
2.59-2.7311.920.493.35541146290.99100
2.73-2.911.930.3374.95518645970.97100
2.9-3.1211.930.2367.15537246040.93100
3.12-3.4311.920.13511.65519545990.85100
3.43-3.9311.950.10115.75552646170.82100
3.93-4.9411.290.0820.95282046270.9399.4
4.94-22.049.820.06527.33970439111.1282.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MZ0 (apo-IDH)

3mz0


Resolution: 2.3003→22.036 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7192 / SU ML: 0.94 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 2325 5.14 %RANDOM
Rwork0.24 ---
all0.2424 ---
obs0.24 45235 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.489 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 161.33 Å2 / Biso mean: 81.4768 Å2 / Biso min: 41.07 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3003→22.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 88 124 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045470
X-RAY DIFFRACTIONf_angle_d0.7827434
X-RAY DIFFRACTIONf_chiral_restr0.057834
X-RAY DIFFRACTIONf_plane_restr0.003948
X-RAY DIFFRACTIONf_dihedral_angle_d17.3862080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3003-2.34720.37991450.341625752720100
2.3472-2.39820.37811330.333925162649100
2.3982-2.45390.35191270.32325912718100
2.4539-2.51520.36531380.318125432681100
2.5152-2.58310.37391170.327525662683100
2.5831-2.6590.39541540.318525732727100
2.659-2.74460.39971260.314925692695100
2.7446-2.84250.42521480.308425272675100
2.8425-2.95610.34191550.306325752730100
2.9561-3.09030.30121360.276725512687100
3.0903-3.25270.34441430.281725682711100
3.2527-3.45580.29681410.248125412682100
3.4558-3.72140.30091380.227125892727100
3.7214-4.09380.25641280.20825942722100
4.0938-4.68120.2191570.18172529268699
4.6812-5.87920.21161440.16612587273199
5.8792-22.03720.2252950.19551916201171

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