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- PDB-2dtx: Structure of Thermoplasma acidophilum aldohexose dehydrogenase (A... -

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Basic information

Entry
Database: PDB / ID: 2dtx
TitleStructure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with D-mannose
ComponentsGlucose 1-dehydrogenase related protein
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Glucose 1-dehydrogenase related protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYasutake, Y. / Nishiya, Y. / Tamura, N. / Tamura, T.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Insights into Unique Substrate Selectivity of Thermoplasma acidophilumd-Aldohexose Dehydrogenase
Authors: Yasutake, Y. / Nishiya, Y. / Tamura, N. / Tamura, T.
History
DepositionJul 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose 1-dehydrogenase related protein
B: Glucose 1-dehydrogenase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6216
Polymers58,0682
Non-polymers5524
Water6,864381
1
A: Glucose 1-dehydrogenase related protein
B: Glucose 1-dehydrogenase related protein
hetero molecules

A: Glucose 1-dehydrogenase related protein
B: Glucose 1-dehydrogenase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,24112
Polymers116,1374
Non-polymers1,1058
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area20280 Å2
ΔGint-198 kcal/mol
Surface area32420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.879, 81.879, 138.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glucose 1-dehydrogenase related protein / Aldohexose dehydrogenase


Mass: 29034.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0754 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9HK51, EC: 1.1.1.118
#2: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 16% PEG 3350, 0.2M AMMONIUM SULFATE, 20% GLYCEROL, 0.1M SODIUM ACETATE, 4MM NADH, 0.1M D-MANNOSE, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 71448 / % possible obs: 99.8 % / Redundancy: 8.4 % / Biso Wilson estimate: 17.982 Å2 / Rsym value: 0.07 / Net I/σ(I): 34.648
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 6.739 / Num. unique all: 6963 / Rsym value: 0.275 / % possible all: 98.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DTE

2dte


Resolution: 1.6→40 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 3604 5.1 %RANDOM
Rwork0.1984 ---
all-71296 --
obs-71296 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0224 Å2 / ksol: 0.381091 e/Å3
Displacement parametersBiso mean: 21.4786 Å2
Baniso -1Baniso -2Baniso -3
1--2.005 Å2-0.991 Å20 Å2
2---2.005 Å20 Å2
3---4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 30 381 4356
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.010219
X-RAY DIFFRACTIONc_angle_deg1.42904
X-RAY DIFFRACTIONc_dihedral_angle_d22.75219
X-RAY DIFFRACTIONc_improper_angle_d1.05738
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 1.6→1.65 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2907 365 5.2 %
Rwork0.2466 6591 -
obs-6956 98.59 %

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