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- PDB-3ajr: Crystal structure of L-3-Hydroxynorvaline bound L-Threonine dehyd... -

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Basic information

Entry
Database: PDB / ID: 3ajr
TitleCrystal structure of L-3-Hydroxynorvaline bound L-Threonine dehydrogenase (Y137F) from Hyperthermophilic Archaeon Thermoplasma volcanium
ComponentsNDP-sugar epimerase
KeywordsOXIDOREDUCTASE / L-threonine dehydrogenase / Thermoplasma volcanium / L-3-Hydroxynorvaline
Function / homology
Function and homology information


L-threonine 3-dehydrogenase activity / L-threonine catabolic process / nucleotide 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 / (3R)-3-hydroxy-L-norvaline / NDP-sugar epimerase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsYoneda, K. / Sakuraba, H. / Ohshima, T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Binary and Ternary Complexes of Archaeal UDP-galactose 4-Epimerase-like L-Threonine Dehydrogenase from Thermoplasma volcanium.
Authors: Yoneda, K. / Sakuraba, H. / Araki, T. / Ohshima, T.
History
DepositionJun 14, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 1, 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: NDP-sugar epimerase
B: NDP-sugar epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5738
Polymers71,7442
Non-polymers1,8296
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-17 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.567, 46.588, 89.929
Angle α, β, γ (deg.)90.00, 113.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

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Components

#1: Protein NDP-sugar epimerase / L-threonine dehydrogenase


Mass: 35871.891 Da / Num. of mol.: 2 / Mutation: Y137F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Strain: GSS1 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q97BK3, L-threonine 3-dehydrogenase
#2: Chemical ChemComp-VAH / (3R)-3-hydroxy-L-norvaline / L-3-Hydroxynorvaline


Type: L-peptide linking / Mass: 133.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 50% MPD, 0.1M SODIUM CACODYLATE(PH6.4), 5% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→82.761 Å / Num. obs: 54564 / % possible obs: 97.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.048
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 4.9 % / Rsym value: 0.146 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A9W

3a9w


Resolution: 1.77→33.914 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2647913.01 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 5551 10.2 %RANDOM
Rwork0.199 ---
obs0.199 54563 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0396 Å2 / ksol: 0.377828 e/Å3
Displacement parametersBiso max: 63.44 Å2 / Biso mean: 24.8 Å2 / Biso min: 11.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.05 Å2
2--0.07 Å20 Å2
3----0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.77→33.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 122 243 5329
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it0.9661.5
X-RAY DIFFRACTIONc_mcangle_it1.5252
X-RAY DIFFRACTIONc_scbond_it2.5133
X-RAY DIFFRACTIONc_scangle_it3.824.5
LS refinement shellResolution: 1.77→1.88 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 908 10.5 %
Rwork0.231 7740 -
all-8648 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4nad.param
X-RAY DIFFRACTION5MPD-NOV.param

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