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- PDB-8hyh: Structure of amino acid dehydrogenase3448 -

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Basic information

Entry
Database: PDB / ID: 8hyh
TitleStructure of amino acid dehydrogenase3448
ComponentsAlanine dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / amino acid / Rossmann fold / NAD
Function / homology
Function and homology information


alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / nucleotide binding
Similarity search - Function
Alanine dehydrogenase / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRUVIC ACID / Alanine dehydrogenase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsSakuraba, H. / Ohshima, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2023
Title: Two different alanine dehydrogenases from Geobacillus kaustophilus: Their biochemical characteristics and differential expression in vegetative cells and spores.
Authors: Maeno, M. / Ohmori, T. / Nukada, D. / Sakuraba, H. / Satomura, T. / Ohshima, T.
History
DepositionJan 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6345
Polymers39,7591
Non-polymers8764
Water2,936163
1
A: Alanine dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)243,80630
Polymers238,5526
Non-polymers5,25424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area29280 Å2
ΔGint-46 kcal/mol
Surface area73920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.621, 149.621, 137.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Alanine dehydrogenase


Mass: 39758.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: GK3448 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KUA3
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: iron (III) chloride, Jeffamine M-600, sodium citrate buffer, NAD, pyruvate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→49.02 Å / Num. obs: 36433 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.035 / Rrim(I) all: 0.158 / Χ2: 0.98 / Net I/σ(I): 21.1 / Num. measured all: 716056
Reflection shellResolution: 2.39→2.48 Å / % possible obs: 99.9 % / Redundancy: 18.5 % / Rmerge(I) obs: 1.677 / Num. measured all: 69276 / Num. unique obs: 3740 / CC1/2: 0.714 / Rpim(I) all: 0.397 / Rrim(I) all: 1.724 / Χ2: 0.99 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→48.97 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.345 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21121 1778 4.9 %RANDOM
Rwork0.18381 ---
obs0.18517 34633 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.986 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å2-0 Å2
2--0.66 Å20 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 2.39→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 58 163 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132819
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162772
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.6433840
X-RAY DIFFRACTIONr_angle_other_deg1.4531.5796362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7075364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00422.869122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84215452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1491515
X-RAY DIFFRACTIONr_chiral_restr0.090.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
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_it4.9424.9371462
X-RAY DIFFRACTIONr_mcbond_other4.9264.9321460
X-RAY DIFFRACTIONr_mcangle_it6.5817.3981823
X-RAY DIFFRACTIONr_mcangle_other6.567.3991823
X-RAY DIFFRACTIONr_scbond_it6.5235.7121355
X-RAY DIFFRACTIONr_scbond_other6.4635.7111354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2118.32015
X-RAY DIFFRACTIONr_long_range_B_refined10.35260.2893068
X-RAY DIFFRACTIONr_long_range_B_other10.35860.2153045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 139 -
Rwork0.3 2509 -
obs--99.85 %

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