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- PDB-3ohs: Crystal Structure of Mammalian Dimeric Dihydrodiol Dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 3ohs
TitleCrystal Structure of Mammalian Dimeric Dihydrodiol Dehydrogenase in complex with Dihydroxyacetone
ComponentsTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase
KeywordsOXIDOREDUCTASE / Dimeric dihydrodiol dehydrogenase / MDD
Function / homology
Function and homology information


D-xylose 1-dehydrogenase (NADP+, D-xylono-1,5-lactone-forming) / D-xylose 1-dehydrogenase (NADP+) activity / D-xylose catabolic process / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase 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
Dihydroxyacetone / BETA-MERCAPTOETHANOL / Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhao, H.-T. / El-Kabbani, O.
CitationJournal: To be Published
Title: Crystal structure of MDD in complex with Dihydroxyacetone
Authors: Zhao, H.-T. / El-Kabbani, O. / Hara, A.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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

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Assembly

Deposited unit
X: Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,41811
Polymers36,4811
Non-polymers93710
Water8,287460
1
X: Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
hetero molecules

X: Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,83522
Polymers72,9622
Non-polymers1,87320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area2760 Å2
ΔGint-18 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.446, 122.446, 121.388
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11X-285-

HOH

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Components

#1: Protein Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / Dimeric dihydrodiol dehydrogenase / D-xylose-NADP dehydrogenase / D-xylose 1-dehydrogenase / Cmo2DD


Mass: 36481.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: DHDH, 2DD / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9TQS6, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, D-xylose 1-dehydrogenase (NADP+, D-xylono-1,5-lactone-forming)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Sugar ChemComp-2HA / Dihydroxyacetone


Type: saccharide / Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 3.6 Å3/Da / Density % sol: 65.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2M ammonium sulfate, 0.1M Tris, pH 8.5, 8% PEG 8000, Vapor Diffusion, Hanging Drop, Temperature 295K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2008 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 39010 / Num. obs: 38518 / % possible obs: 98.74 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.65 % / Rmerge(I) obs: 0.0571 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.43 % / Rmerge(I) obs: 0.3863 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3343 / % possible all: 85.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O4U

2o4u


Resolution: 1.9→29.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.478 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Ser X 1009 is within close proximity to sulphate ion (1 SO4) causing deviations in TORSION ANGLES
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 1991 4.9 %RANDOM
Rwork0.1611 ---
obs0.16325 38518 98.74 %-
all-39010 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.654 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.211 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 50 460 3039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222802
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9843853
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67923.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02615484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7641521
X-RAY DIFFRACTIONr_chiral_restr0.1640.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212121
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2141.51750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92422846
X-RAY DIFFRACTIONr_scbond_it3.28131052
X-RAY DIFFRACTIONr_scangle_it4.8864.5973
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 104 -
Rwork0.294 2337 -
obs-3349 93.92 %

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