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- PDB-4yrb: mouse TDH mutant R180K with NAD+ bound -

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Basic information

Entry
Database: PDB / ID: 4yrb
Titlemouse TDH mutant R180K with NAD+ bound
ComponentsL-threonine 3-dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / L-threonine 3-dehydrogenase
Function / homology
Function and homology information


L-threonine 3-dehydrogenase / L-threonine catabolic process to glycine / L-threonine 3-dehydrogenase activity / L-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: 3.25 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)224,22212
Polymers220,2416
Non-polymers3,9816
Water00
1
A: L-threonine 3-dehydrogenase, mitochondrial
B: L-threonine 3-dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7414
Polymers73,4142
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-23 kcal/mol
Surface area18150 Å2
MethodPISA
2
C: L-threonine 3-dehydrogenase, mitochondrial
D: L-threonine 3-dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7414
Polymers73,4142
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-22 kcal/mol
Surface area21370 Å2
MethodPISA
3
E: L-threonine 3-dehydrogenase, mitochondrial
F: L-threonine 3-dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7414
Polymers73,4142
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-23 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.240, 154.050, 199.190
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: 36706.875 Da / Num. of mol.: 6 / Fragment: UNP residues 47-373 / Mutation: R180K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdh / Production host: Escherichia coli (E. coli) / 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

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris, 20%(w/v) Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.25→121.859 Å / Num. all: 35778 / Num. obs: 35778 / % possible obs: 97.4 % / Redundancy: 4 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.153 / Rsym value: 0.134 / Net I/av σ(I): 4.794 / Net I/σ(I): 8.6 / Num. measured all: 144642
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
3.25-3.433.50.5661.31710249520.3250.5662.494.3
3.43-3.633.60.381.41724948160.2210.383.796.4
3.63-3.883.70.272.71721046220.1520.275.197.7
3.88-4.23.90.1893.21672443090.1040.1896.898.3
4.2-4.640.135.71570439690.070.138.997.4
4.6-5.144.40.0997.41555635390.050.09911.895.9
5.14-5.934.80.10671558232750.0530.10611.699.8
5.93-7.274.80.0937.91346828060.0470.09313.199.9
7.27-10.284.70.04712.31050022190.0240.04720.499.7
10.28-47.1194.40.04411554712710.0240.04422.697.9

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YR9

4yr9


Resolution: 3.25→47.12 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.849 / WRfactor Rfree: 0.2624 / WRfactor Rwork: 0.2111 / FOM work R set: 0.8138 / SU B: 23.843 / SU ML: 0.404 / SU Rfree: 0.5385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.539 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 1772 5 %RANDOM
Rwork0.2276 ---
obs0.2305 33952 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 176.23 Å2 / Biso mean: 76.453 Å2 / Biso min: 37.63 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 3.25→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10592 0 264 0 10856
Biso mean--94.05 --
Num. residues----1333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911132
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210524
X-RAY DIFFRACTIONr_angle_refined_deg1.061.98915143
X-RAY DIFFRACTIONr_angle_other_deg0.716324054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85251309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19722.14486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.004151757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4091597
X-RAY DIFFRACTIONr_chiral_restr0.0550.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022707
X-RAY DIFFRACTIONr_mcbond_it2.7247.6475308
X-RAY DIFFRACTIONr_mcbond_other2.7237.6465307
X-RAY DIFFRACTIONr_mcangle_it4.63111.4476593
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 106 -
Rwork0.286 2351 -
all-2457 -
obs--92.89 %

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