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- PDB-3ntq: Crystal structure of K97V mutant myo-inositol dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 3ntq
TitleCrystal structure of K97V mutant myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NAD
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
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: 2.6004 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)78,0564
Polymers76,7292
Non-polymers1,3272
Water84747
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)156,1128
Polymers153,4584
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area16920 Å2
ΔGint-68 kcal/mol
Surface area50500 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)234,16712
Polymers230,1876
Non-polymers3,9816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area17200 Å2
ΔGint-94 kcal/mol
Surface area83930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.387, 184.387, 184.387
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 45:73 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)A0
212CHAIN 'B' AND (RESSEQ 45:73 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)B0
113CHAIN 'A' AND (RESSEQ 76:337 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)A0
213CHAIN 'B' AND (RESSEQ 76:337 ) 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 63.87 %
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: 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: 2.6→19.883 Å / Num. obs: 31891 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.092 / Χ2: 0.98 / Net I/σ(I): 8 / Scaling rejects: 1566
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.6-2.696.360.8561.62027931761.43100
2.69-2.86.620.7441.72105331771.06100
2.8-2.936.610.5972.22097831701.03100
2.93-3.086.60.4852.82118031941.01100
3.08-3.276.60.32542107431800.99100
3.27-3.536.450.2156.32102132021.06100
3.53-3.886.450.1498.42097131890.9599.9
3.88-4.436.50.08713.82113832300.76100
4.43-5.576.550.07715.22112732060.7299.6
5.57-19.886.20.04924.81989031670.8196

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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: 2.6004→19.883 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7372 / SU ML: 0.48 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 1645 5.16 %RANDOM
Rwork0.2297 ---
obs0.2315 31882 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.806 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 181.98 Å2 / Biso mean: 91.5175 Å2 / Biso min: 41.42 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6004→19.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 88 47 5411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095466
X-RAY DIFFRACTIONf_angle_d1.1657432
X-RAY DIFFRACTIONf_chiral_restr0.079836
X-RAY DIFFRACTIONf_plane_restr0.005948
X-RAY DIFFRACTIONf_dihedral_angle_d19.6922070
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A291X-RAY DIFFRACTIONPOSITIONAL0.044
12B291X-RAY DIFFRACTIONPOSITIONAL0.044
21A225X-RAY DIFFRACTIONPOSITIONAL0.036
22B225X-RAY DIFFRACTIONPOSITIONAL0.036
31A2072X-RAY DIFFRACTIONPOSITIONAL0.043
32B2072X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6004-2.69310.39841530.350530233176100
2.6931-2.80060.38561590.335330183177100
2.8006-2.92770.35561830.309729873170100
2.9277-3.08150.37871740.302630203194100
3.0815-3.27380.3291660.286330143180100
3.2738-3.52530.33351870.254330153202100
3.5253-3.87770.29071420.249430473189100
3.8777-4.43340.26651460.210830833229100
4.4334-5.56520.1911690.185330353204100
5.5652-19.88350.21041660.18432995316196

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