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- PDB-3cea: Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) f... -

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Basic information

Entry
Database: PDB / ID: 3cea
TitleCrystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from Lactobacillus plantarum at 2.40 A resolution
ComponentsMyo-inositol 2-dehydrogenase
KeywordsOXIDOREDUCTASE / NP_786804.1 / myo-inositol 2-dehydrogenase / Oxidoreductase family / NAD-binding Rossmann fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding
Similarity search - Function
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 ...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 / Myo-inositol 2-dehydrogenase-like (Promiscuous) / :
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from Lactobacillus plantarum at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)157,72812
Polymers154,8534
Non-polymers2,8758
Water6,179343
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-70.1 kcal/mol
Surface area49080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.331, 145.684, 100.208
Angle α, β, γ (deg.)90.000, 91.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRLEU4AA4 - 3455 - 346
2THRLEU4BB4 - 3455 - 346
3LYSGLN6CC6 - 3447 - 345
4LYSGLN6DD6 - 3447 - 345
DetailsAUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Myo-inositol 2-dehydrogenase


Mass: 38713.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarumLactiplantibacillus plantarum
Strain: WCFS1 / NCIMB 8826 / Gene: NP_786804.1, iolG1, lp_3605 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q88S39, UniProt: F9ULF9*PLUS, inositol 2-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.2M MgCl2, 20.0% PEG 1000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97941, 0.97883
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 10, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
30.978831
ReflectionResolution: 2.4→29.45 Å / Num. obs: 52411 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.924 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.4620.4291.9702134670.42991.8
2.46-2.5320.3881.9731535750.38894.5
2.53-2.63.80.5171.41440437460.517100
2.6-2.683.90.4471.61384435920.447100
2.68-2.773.80.36421337034840.364100
2.77-2.873.90.2932.51308233830.293100
2.87-2.983.90.2652.81264432830.265100
2.98-3.13.90.2173.41207331240.217100
3.1-3.243.90.1764.21160630050.176100
3.24-3.393.90.1395.31131129350.139100
3.39-3.583.90.1116.51047727120.111100
3.58-3.793.90.0927.8995125770.092100
3.79-4.063.90.0838.6945724530.083100
4.06-4.383.80.0778.8880422900.077100
4.38-4.83.80.0728.9809121040.072100
4.8-5.373.90.0729.6727218880.072100
5.37-6.23.90.089645216700.08100
6.2-7.593.80.06910.3544214220.069100
7.59-10.733.80.04813.4421011060.048100
10.73-29.453.60.04513.521715950.04595.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.45 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 19.09 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.655 / ESU R Free: 0.28
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO MOLECULE FROM THE CRYO SOLUTION IS MODELED. 4. LIGAND MOLECULE NAD IS MODELED IN EACH MONOMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2662 5.1 %RANDOM
Rwork0.193 ---
obs0.196 52383 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.891 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å20 Å2-0.01 Å2
2---2.35 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10435 0 189 343 10967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210863
X-RAY DIFFRACTIONr_angle_refined_deg0.9341.96314764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.65351368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84124.921504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.561151748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.61556
X-RAY DIFFRACTIONr_chiral_restr0.0570.21654
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028280
X-RAY DIFFRACTIONr_nbd_refined0.1680.25056
X-RAY DIFFRACTIONr_nbtor_refined0.2920.27472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2511
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.10.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0460.22
X-RAY DIFFRACTIONr_mcbond_it0.40926941
X-RAY DIFFRACTIONr_mcangle_it0.752410851
X-RAY DIFFRACTIONr_scbond_it1.31764416
X-RAY DIFFRACTIONr_scangle_it1.98783908
Refine LS restraints NCS

Ens-ID: 1 / Number: 2533 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.385
2BLOOSE POSITIONAL0.375
3CLOOSE POSITIONAL0.45
4DLOOSE POSITIONAL0.365
1ALOOSE THERMAL0.9810
2BLOOSE THERMAL1.0510
3CLOOSE THERMAL1.0310
4DLOOSE THERMAL1.0810
LS refinement shellResolution: 2.4→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 199 -
Rwork0.273 3439 -
all-3638 -
obs--92.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.65920.06060.27880.9543-0.25821.60130.01170.15150.1153-0.3372-0.06430.02490.04450.11920.0526-0.06420.02020.0304-0.03060.0524-0.069716.254985.305651.8442
20.3708-0.2266-0.03351.1561-0.34321.392-0.0185-0.0787-0.08430.3785-0.01750.038-0.0689-0.03030.036-0.1323-0.0312-0.0066-0.04910.0489-0.06639.928653.432498.408
30.960.0576-0.07421.460.02631.16440.04210.147-0.1202-0.5466-0.04880.1190.1239-0.04650.0067-0.00460.0176-0.0561-0.0747-0.0349-0.05674.424349.247456.4922
40.3379-0.31880.30921.0690.31231.7028-0.0827-0.08830.07720.22070.0258-0.003-0.2334-0.1040.0568-0.13340.01680.0228-0.0673-0.0431-0.00899.927391.443893.4395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 3455 - 346
2X-RAY DIFFRACTION2BB4 - 3455 - 346
3X-RAY DIFFRACTION3CC6 - 3447 - 345
4X-RAY DIFFRACTION4DD6 - 3447 - 345

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