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

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Basic information

Entry
Database: PDB / ID: 2dte
TitleStructure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with NADH
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Glucose 1-dehydrogenase related protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 12, 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: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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: Glucose 1-dehydrogenase related protein
B: Glucose 1-dehydrogenase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3994
Polymers58,0682
Non-polymers1,3312
Water6,017334
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)118,7988
Polymers116,1374
Non-polymers2,6624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area22410 Å2
ΔGint-174 kcal/mol
Surface area31900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.511, 81.511, 138.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a homotetramer generated from the dimer in the asymmetric unit by the operations: x-y, -y, -z+1/3.

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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: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
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, 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-5A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 64639 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 19.86 Å2 / Rsym value: 0.049 / Net I/σ(I): 29.3
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 6.4 / Num. unique all: 6422 / Rsym value: 0.371 / % possible all: 100

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Processing

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

1gco


Resolution: 1.65→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 3251 5 %RANDOM
Rwork0.1955 ---
all-64586 --
obs-64586 99.9 %-
Displacement parametersBiso mean: 23.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å2-1.675 Å20 Å2
2---2.88 Å20 Å2
3---5.76 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: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 88 334 4326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007291
X-RAY DIFFRACTIONc_angle_deg1.38752
X-RAY DIFFRACTIONc_dihedral_angle_d22.2244
X-RAY DIFFRACTIONc_improper_angle_d0.92964
X-RAY DIFFRACTIONc_mcbond_it1.151
X-RAY DIFFRACTIONc_mcangle_it1.801
X-RAY DIFFRACTIONc_scbond_it1.938
X-RAY DIFFRACTIONc_scangle_it2.862
LS refinement shellResolution: 1.65→1.71 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2568 335 5.23 %
Rwork0.2361 6031 -
obs-6366 99.32 %

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