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- PDB-9vae: Crystal structure of alanine dehydrogenase-like protein from Ther... -

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Basic information

Entry
Database: PDB / ID: 9vae
TitleCrystal structure of alanine dehydrogenase-like protein from Thermus thermophilus
Componentsalanine dehydrogenase
KeywordsSIGNALING PROTEIN / alanine dehydrogenase-like protein / NAD(H)-binding protein
Function / homology
Function and homology information


alanine dehydrogenase / L-alanine dehydrogenase (NAD+) activity / L-alanine catabolic process / plasma membrane
Similarity search - Function
Alanine dehydrogenase / 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 / alanine dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYoshida, A. / Yamamoto, H. / Nishiyama, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17J40083 Japan
Japan Society for the Promotion of Science (JSPS)20K05804 Japan
CitationJournal: To Be Published
Title: Catalytic regulation of CoA transferase by an NAD+-sensing accessory protein and protein acetylation
Authors: Yoshida, A. / Yamamoto, H. / Nishiyama, M.
History
DepositionJun 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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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)37,1052
Polymers36,4411
Non-polymers6631
Water1,18966
1
A: alanine dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)222,62712
Polymers218,6476
Non-polymers3,9816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area20980 Å2
ΔGint-116 kcal/mol
Surface area72860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.060, 86.060, 178.203
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-566-

HOH

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Components

#1: Protein alanine dehydrogenase


Mass: 36441.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72IQ0, alanine dehydrogenase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.5 Å / Num. obs: 14250 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.03 / Rrim(I) all: 0.131 / Χ2: 0.98 / Net I/σ(I): 18.1
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 100 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.857 / Num. measured all: 30547 / Num. unique obs: 1551 / CC1/2: 0.967 / Rpim(I) all: 0.196 / Rrim(I) all: 0.88 / Χ2: 0.95 / Net I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.5 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.873 / SU B: 10.571 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28578 696 4.9 %RANDOM
Rwork0.22517 ---
obs0.22812 13520 99.94 %-
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: 57.067 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20.93 Å20 Å2
2--1.86 Å20 Å2
3----6.02 Å2
Refinement stepCycle: 1 / Resolution: 2.5→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 44 66 2610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132594
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152561
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.653532
X-RAY DIFFRACTIONr_angle_other_deg1.0431.5675877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42619.444126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41615406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0281528
X-RAY DIFFRACTIONr_chiral_restr0.0410.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
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_it1.5346.0041350
X-RAY DIFFRACTIONr_mcbond_other1.5356.0031349
X-RAY DIFFRACTIONr_mcangle_it2.6589.0021683
X-RAY DIFFRACTIONr_mcangle_other2.6579.0031684
X-RAY DIFFRACTIONr_scbond_it1.396.2491244
X-RAY DIFFRACTIONr_scbond_other1.396.2481245
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.469.261849
X-RAY DIFFRACTIONr_long_range_B_refined4.48570.3392598
X-RAY DIFFRACTIONr_long_range_B_other4.48170.3372596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 51 -
Rwork0.278 961 -
obs--99.8 %

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