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- PDB-4hkt: Crystal structure of a putative myo-inositol dehydrogenase from S... -

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Basic information

Entry
Database: PDB / ID: 4hkt
TitleCrystal structure of a putative myo-inositol dehydrogenase from Sinorhizobium meliloti 1021 (Target PSI-012312)
ComponentsInositol 2-dehydrogenase
KeywordsOXIDOREDUCTASE / Structural genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


inositol 2-dehydrogenase / inositol 2-dehydrogenase (NAD+) activity
Similarity search - Function
Inositol 2-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 ...Inositol 2-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
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a putative myo-inositoldehydrogenase from Sinorhizobium meliloti 1021 (Target PSI-012312)
Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / ...Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Almo, S.C.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol 2-dehydrogenase
B: Inositol 2-dehydrogenase
C: Inositol 2-dehydrogenase
D: Inositol 2-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,29733
Polymers142,4254
Non-polymers1,87229
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-2 kcal/mol
Surface area47750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.449, 55.467, 149.091
Angle α, β, γ (deg.)90.000, 97.560, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a probable tetramer

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Components

#1: Protein
Inositol 2-dehydrogenase / / Myo-inositol 2-dehydrogenase / MI-dehydrogenase


Mass: 35606.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: idhA, iolG, RB1194, SMb20899, SM_b20899 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: O68965, inositol 2-dehydrogenase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (MCSG1 #93; H9: 0.1 M Bis-Tris:HCl pH 5.5, 25% (w/v) PEG 3350 ), Cryoprotection (30% Ethylene glycol), VAPOR DIFFUSION, ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (MCSG1 #93; H9: 0.1 M Bis-Tris:HCl pH 5.5, 25% (w/v) PEG 3350 ), Cryoprotection (30% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2012 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 99392 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.086 / Net I/σ(I): 16.87
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.64 / Num. unique all: 4809 / Rsym value: 0.528 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0025refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→41 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.03 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 4995 5 %RANDOM
Rwork0.1857 ---
obs0.188 99374 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 113.88 Å2 / Biso mean: 35.4543 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å2-0.06 Å2
2---0.08 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9852 0 120 632 10604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910189
X-RAY DIFFRACTIONr_bond_other_d0.0020.029947
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.97113760
X-RAY DIFFRACTIONr_angle_other_deg0.759322794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80251337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.622.886440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.571151579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.13715102
X-RAY DIFFRACTIONr_chiral_restr0.0830.21584
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022262
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 349 -
Rwork0.228 6716 -
all-7065 -
obs--96.1 %

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