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- PDB-3nt5: Crystal structure of myo-inositol dehydrogenase from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 3nt5
TitleCrystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor and product inosose
ComponentsInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
KeywordsOXIDOREDUCTASE / BSIDH / N-terminal Rossmann fold domain / glyceraldehyde-3-phosphate like C-terminal domain / NAD(H) / inositol / inosose
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
Chem-ISE / 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: 2.9006 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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)78,4746
Polymers76,7892
Non-polymers1,6854
Water00
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)156,94812
Polymers153,5784
Non-polymers3,3708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area16700 Å2
ΔGint-74 kcal/mol
Surface area50260 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)235,42318
Polymers230,3676
Non-polymers5,05512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area17230 Å2
ΔGint-100 kcal/mol
Surface area83220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.498, 183.498, 183.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 1:40 ) and (not element H) and (not element D)A0
211chain 'B' and (resseq 1:40 ) and (not element H) and (not element D)B0
112chain 'A' and (resseq 48:74 ) and (not element H) and (not element D)A0
212chain 'B' and (resseq 48:74 ) and (not element H) and (not element D)B0
113chain 'A' and (resseq 76:117 ) and (not element H) and (not element D)A0
213chain 'B' and (resseq 76:117 ) and (not element H) and (not element D)B0
114chain 'A' and (resseq 120:337 ) and (not element H) and (not element D)A0
214chain 'B' and (resseq 120:337 ) and (not element H) and (not element D)B0

NCS ensembles :
ID
1
2
3
4

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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-ISE / (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone / Inosose / Myo-inosose


Mass: 178.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O6
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2

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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: 3.35 Å3/Da / Density % sol: 63.31 %
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: 2.8→39.122 Å / Num. obs: 25421 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.38 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.13 / Χ2: 0.92 / Net I/σ(I): 8.2 / Scaling rejects: 4878
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2
2.8-2.922.80.9051.35808025401.17
2.9-3.0222.810.8691.65754925171.19
3.02-3.1522.760.7752.25727025081.21
3.15-3.3222.660.6053.15694725031.13
3.32-3.5322.510.464.35776825501.03
3.53-3.822.320.3215.85672825150.93
3.8-4.1822.160.1899.55747025510.8
4.18-4.7922.180.10914.35722225340.65
4.79-6.0322.170.10715.15751225560.6
6.03-39.1221.490.05225.45725226470.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.0Ldata scaling
MOLREPphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MZ0 (apo-IDH)

3mz0


Resolution: 2.9006→39.122 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7419 / SU ML: 0.44 / Isotropic thermal model: B group / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2912 1170 5.12 %RANDOM
Rwork0.2408 ---
obs0.2434 22866 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.123 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 236.35 Å2 / Biso mean: 111.7268 Å2 / Biso min: 43.58 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.9006→39.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 112 0 5392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015494
X-RAY DIFFRACTIONf_angle_d1.3357470
X-RAY DIFFRACTIONf_chiral_restr0.08844
X-RAY DIFFRACTIONf_plane_restr0.005950
X-RAY DIFFRACTIONf_dihedral_angle_d20.0762128
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A291X-RAY DIFFRACTIONPOSITIONAL0.038
12B291X-RAY DIFFRACTIONPOSITIONAL0.038
21A206X-RAY DIFFRACTIONPOSITIONAL0.033
22B206X-RAY DIFFRACTIONPOSITIONAL0.033
31A317X-RAY DIFFRACTIONPOSITIONAL0.037
32B317X-RAY DIFFRACTIONPOSITIONAL0.037
41A1737X-RAY DIFFRACTIONPOSITIONAL0.039
42B1737X-RAY DIFFRACTIONPOSITIONAL0.039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9006-3.03260.34181470.318526742821
3.0326-3.19240.33351400.327926902830
3.1924-3.39230.3591500.307826982848
3.3923-3.65410.36091420.307326902832
3.6541-4.02150.34491330.278827062839
4.0215-4.60260.25991620.225727112873
4.6026-5.79580.23711400.204827252865
5.7958-39.12540.26981560.200828022958

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