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- PDB-3ntr: Crystal structure of K97V mutant of myo-inositol dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 3ntr
TitleCrystal structure of K97V mutant of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NAD and inositol
ComponentsInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
KeywordsOXIDOREDUCTASE / K97V mutant / BSIDH / N-terminal Rossmann fold domain / glyceraldehyde-3-phosphate like C-terminal domain
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
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / NICOTINAMIDE-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: 2.6503 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 5, 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4166
Polymers76,7292
Non-polymers1,6874
Water1,00956
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)156,83212
Polymers153,4584
Non-polymers3,3748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_554x,-y,-z-1/21
Buried area18660 Å2
ΔGint-66 kcal/mol
Surface area50480 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)235,24818
Polymers230,1876
Non-polymers5,06112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area19990 Å2
ΔGint-91 kcal/mol
Surface area83720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.695, 183.695, 183.695
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

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 45:70 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)A0
212CHAIN 'B' AND (RESSEQ 45:70 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)B0
113CHAIN 'A' AND (RESSEQ 80:337 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)A0
213CHAIN 'B' AND (RESSEQ 80:337 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)B0

NCS ensembles :
ID
1
2
3

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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: 38364.488 Da / Num. of mol.: 2 / Mutation: K97V
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.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.4
Details: 0.1M tri-sodium citrate pH 5.4, 2M 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: Jun 16, 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: 2.65→19.81 Å / Num. obs: 29913 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.59 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.15 / Χ2: 0.96 / Net I/σ(I): 6.4 / Scaling rejects: 2394
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2
2.65-2.748.230.8691.52434529571.09
2.74-2.859.340.8381.62767429611.04
2.85-2.9810.590.7971.93146729701.06
2.98-3.1411.390.7052.33384329690.98
3.14-3.3411.360.5433381429710.99
3.34-3.5911.190.4094.33350529621.1
3.59-3.9511.030.2855.93384030171.05
3.95-4.5211.10.1598.73334529870.81
4.52-5.6711.060.11411.93374130230.75
5.67-19.8110.560.06720.23354530960.76

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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 3NT2 (holo-IDH)

3nt2


Resolution: 2.6503→19.808 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6463 / SU ML: 0.57 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 1544 5.16 %RANDOM
Rwork0.2315 ---
obs0.2339 29907 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.636 Å2 / ksol: 0.27 e/Å3
Displacement parametersBiso max: 185.76 Å2 / Biso mean: 102.8081 Å2 / Biso min: 46.28 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6503→19.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 112 56 5444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015490
X-RAY DIFFRACTIONf_angle_d1.2537468
X-RAY DIFFRACTIONf_chiral_restr0.079836
X-RAY DIFFRACTIONf_plane_restr0.004948
X-RAY DIFFRACTIONf_dihedral_angle_d19.7612106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A291X-RAY DIFFRACTIONPOSITIONAL0.045
12B291X-RAY DIFFRACTIONPOSITIONAL0.045
21A203X-RAY DIFFRACTIONPOSITIONAL0.037
22B203X-RAY DIFFRACTIONPOSITIONAL0.037
31A2046X-RAY DIFFRACTIONPOSITIONAL0.044
32B2046X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6503-2.74480.43391540.42328032957
2.7448-2.85440.43531400.402728212961
2.8544-2.98390.37491590.362128112970
2.9839-3.14060.35591600.333928092969
3.1406-3.33650.35811400.296628302970
3.3365-3.59270.32831640.274127972961
3.5927-3.95170.28291460.249828703016
3.9517-4.51760.28261580.200528292987
4.5176-5.66950.251530.178328703023
5.6695-19.80890.21091700.168129233093

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