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- PDB-4yr9: mouse TDH with NAD+ bound -

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Basic information

Entry
Database: PDB / ID: 4yr9
Titlemouse TDH with NAD+ bound
ComponentsL-threonine 3-dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / L-threonine 3-dehydrogenase
Function / homology
Function and homology information


L-threonine catabolic process to glycine / L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / threonine catabolic process / mitochondrion / identical protein binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-threonine 3-dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHe, C. / Li, F.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural insights on mouse l-threonine dehydrogenase: A regulatory role of Arg180 in catalysis
Authors: He, C. / Huang, X. / Liu, Y. / Li, F. / Yang, Y. / Tao, H. / Han, C. / Zhao, C. / Xiao, Y. / Shi, Y.
History
DepositionMar 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-threonine 3-dehydrogenase, mitochondrial
B: L-threonine 3-dehydrogenase, mitochondrial
C: L-threonine 3-dehydrogenase, mitochondrial
D: L-threonine 3-dehydrogenase, mitochondrial
E: L-threonine 3-dehydrogenase, mitochondrial
F: L-threonine 3-dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,66615
Polymers220,4096
Non-polymers4,2579
Water1,35175
1
A: L-threonine 3-dehydrogenase, mitochondrial
C: L-threonine 3-dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9816
Polymers73,4702
Non-polymers1,5114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-28 kcal/mol
Surface area23810 Å2
MethodPISA
2
B: L-threonine 3-dehydrogenase, mitochondrial
D: L-threonine 3-dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8895
Polymers73,4702
Non-polymers1,4193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-24 kcal/mol
Surface area23780 Å2
MethodPISA
3
E: L-threonine 3-dehydrogenase, mitochondrial
F: L-threonine 3-dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7974
Polymers73,4702
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-26 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.150, 160.130, 194.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
L-threonine 3-dehydrogenase, mitochondrial


Mass: 36734.891 Da / Num. of mol.: 6 / Fragment: UNP residues 47-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdh / Plasmid: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8K3F7, L-threonine 3-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium chloride, 0.1 M HEPES, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.8→123.572 Å / Num. all: 53532 / Num. obs: 53532 / % possible obs: 92.7 % / Redundancy: 4.2 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.115 / Rsym value: 0.101 / Net I/av σ(I): 6.761 / Net I/σ(I): 11 / Num. measured all: 226819
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.9540.5871.32924873290.3060.5872.288.1
2.95-3.133.90.4111.92704869190.2170.4113.188.3
3.13-3.353.80.2512.92508965820.1360.2514.988.5
3.35-3.613.60.1584.82243161670.0870.1587.489.6
3.61-3.963.40.1076.72029259780.0640.10710.593.4
3.96-4.434.20.08682396156390.0460.08614.697.1
4.43-5.114.50.0679.82271550490.0350.06719.298.5
5.11-6.2650.065102219944100.0320.06518.999.6
6.26-8.856.10.05610.82113534640.0240.05623.7100
8.85-38.866.40.04513.41270119950.0190.0453398.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YY7

2yy7


Resolution: 2.8→36.42 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.2445 / WRfactor Rwork: 0.1947 / FOM work R set: 0.8189 / SU B: 16.42 / SU ML: 0.319 / SU Rfree: 0.4183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 2700 5 %RANDOM
Rwork0.2156 ---
obs0.218 50776 92.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.74 Å2 / Biso mean: 49.791 Å2 / Biso min: 12.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.8→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14495 0 282 75 14852
Biso mean--33.56 27.67 -
Num. residues----1839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01915176
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.97920681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95251826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80122.622679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96152342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.66615126
X-RAY DIFFRACTIONr_chiral_restr0.0630.22277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111567
X-RAY DIFFRACTIONr_mcbond_it1.2195.0167343
X-RAY DIFFRACTIONr_mcangle_it2.2037.5149156
X-RAY DIFFRACTIONr_scbond_it0.9324.9677833
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 194 -
Rwork0.31 3504 -
all-3698 -
obs--87.98 %

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