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- PDB-4mie: Crystal Structure of apo myo-inositol dehydrogenase from Lactobac... -

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Basic information

Entry
Database: PDB / ID: 4mie
TitleCrystal Structure of apo myo-inositol dehydrogenase from Lactobacillus casei
ComponentsInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
KeywordsOXIDOREDUCTASE / NAD / sugar alcohol dehydrogenases / Rossmann fold / dehydrogenase / NAD binding / myo-inositol binding / dehydrogenate
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 / Rossmann fold ...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 speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBertwistle, D. / Sanders, D.A.R. / Palmer, D.R.J.
CitationJournal: To be Published
Title: Crystal Structure of apo myo-inositol dehydrogenase from Lactobacillus casei
Authors: Bertwistle, D. / Aamudalapalli, H. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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
C: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
D: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,32422
Polymers154,6424
Non-polymers1,68218
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17450 Å2
ΔGint-146 kcal/mol
Surface area50050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.110, 110.980, 125.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase / Myo-inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase


Mass: 38660.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: BL23 / Gene: idh, iolG, iolG1, LCABL_02210 / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: B3W8L3, UniProt: A0A0J9X1Y2*PLUS, inositol 2-dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: ammonium sulfate, pH 6.5, MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97952 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 27, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2→83.18 Å / Num. all: 101470 / Num. obs: 101470 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 24.97 Å2 / Rsym value: 0.104 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.116.20.5971.290591146030.59799.6
2.11-2.246.40.4241.889137138900.42499.7
2.24-2.396.60.3072.486199130310.30799.9
2.39-2.586.80.2143.583498122030.21499.9
2.58-2.837.10.1674.579725112280.167100
2.83-3.167.30.125.975143102430.12100
3.16-3.657.50.0729.26759790380.072100
3.65-4.477.50.0629.75765177330.062100
4.47-6.327.40.0412.64450060300.04100
6.32-41.5970.03913.32429934710.03999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.15 Å41.59 Å
Translation2.15 Å41.59 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MZ0

3mz0


Resolution: 2→41.59 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8517 / SU ML: 0.11 / σ(F): 1.36 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 5066 5 %RANDOM
Rwork0.1886 ---
obs0.191 101397 99.83 %-
all-101501 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.34 Å2 / Biso mean: 25.7928 Å2 / Biso min: 9.52 Å2
Refinement stepCycle: LAST / Resolution: 2→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10528 0 102 694 11324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01810830
X-RAY DIFFRACTIONf_angle_d1.12814733
X-RAY DIFFRACTIONf_chiral_restr0.1081724
X-RAY DIFFRACTIONf_plane_restr0.0041904
X-RAY DIFFRACTIONf_dihedral_angle_d14.6573935
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.30041590.24773184334399
2.0227-2.04650.30531650.244831633328100
2.0465-2.07150.27551770.23453141331899
2.0715-2.09770.28371790.229931693348100
2.0977-2.12530.24561430.226631613304100
2.1253-2.15440.29821650.22233162332799
2.1544-2.18520.24441540.217332103364100
2.1852-2.21780.25761770.215531553332100
2.2178-2.25250.26321730.209431663339100
2.2525-2.28940.27241570.209932043361100
2.2894-2.32890.25741620.209132033365100
2.3289-2.37120.26491510.209332093360100
2.3712-2.41680.26271490.206731993348100
2.4168-2.46610.23341770.200631873364100
2.4661-2.51980.21291850.203631763361100
2.5198-2.57840.25811440.205532203364100
2.5784-2.64280.24971490.207631873336100
2.6428-2.71430.26571870.208232003387100
2.7143-2.79410.25271910.204132003391100
2.7941-2.88430.24591760.203631743350100
2.8843-2.98730.25141740.201832143388100
2.9873-3.10690.24531630.197132333396100
3.1069-3.24830.25891780.197932053383100
3.2483-3.41950.19521740.173632313405100
3.4195-3.63360.2241650.161232363401100
3.6336-3.91390.19751750.166332483423100
3.9139-4.30740.21541760.146732623438100
4.3074-4.92990.15721770.147432743451100
4.9299-6.20780.19641690.17833223491100
6.2078-41.5990.20241950.179834363631100

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