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

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Basic information

Entry
Database: PDB / ID: 3nto
TitleCrystal structure of K97V mutant myo-inositol dehydrogenase from Bacillus subtilis
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
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9124 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 1.3Dec 27, 2023Group: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,6032
Polymers38,3641
Non-polymers2381
Water6,341352
1
A: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)154,4118
Polymers153,4584
Non-polymers9534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area14310 Å2
ΔGint-24 kcal/mol
Surface area52350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.270, 119.500, 128.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-604-

HOH

31A-618-

HOH

41A-679-

HOH

51A-686-

HOH

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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.: 1 / 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.5
Details: 0.2M CaCl2, 0.1M Hepes pH 7.5, 14% PEG 400, microbatch, temperature 277K

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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 22, 2008
RadiationMonochromator: SAGITALLY FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.91→40 Å / Num. obs: 31224 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 27.557 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 33.41
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.91-1.960.13798354200286.8
1.96-2.020.11315.4160542247100
2.02-2.070.09418.5156092185100
2.07-2.140.08220.7151822124100
2.14-2.210.06723.2147652064100
2.21-2.290.06126142721999100
2.29-2.370.05628.213728192399.9
2.37-2.470.04831.413306186299.9
2.47-2.580.04433.712676177999.9
2.58-2.70.0437.112249171999.9
2.7-2.850.03640.311547163199.9
2.85-3.020.0344410936154899.9
3.02-3.230.03247.510266145499.9
3.23-3.490.02951.396171375100
3.49-3.820.02854.18720125799.9
3.82-4.280.02756.57811113399.9
4.28-4.940.02657.669261025100
4.94-6.050.02457.2594187399.9
6.05-8.550.02356.4446269099.4
8.550.02750.2169633480.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-IDH

Resolution: 1.9124→19.67 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8678 / SU ML: 0.23 / Isotropic thermal model: RANDOM / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1561 5 %RANDOM
Rwork0.1675 ---
obs0.1696 31217 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.722 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 97.74 Å2 / Biso mean: 25.6228 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1-13.2093 Å2-0 Å2-0 Å2
2---4.5027 Å2-0 Å2
3----8.7066 Å2
Refinement stepCycle: LAST / Resolution: 1.9124→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 15 352 3011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072736
X-RAY DIFFRACTIONf_angle_d1.0233716
X-RAY DIFFRACTIONf_chiral_restr0.073422
X-RAY DIFFRACTIONf_plane_restr0.004481
X-RAY DIFFRACTIONf_dihedral_angle_d13.611025
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 (%)
1.9124-1.98070.22641400.19312646278690
1.9807-2.060.23031560.174229643120100
2.06-2.15360.19371550.170829563111100
2.1536-2.2670.24651570.168129813138100
2.267-2.40880.22431570.173429843141100
2.4088-2.59440.21560.169229643120100
2.5944-2.85480.20391580.170429993157100
2.8548-3.26620.21831590.174530223181100
3.2662-4.10890.1811590.151730163175100
4.1089-19.67150.20021640.15833124328899

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