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- PDB-6a0t: Homoserine dehydrogenase K99A mutant from Thermus thermophilus HB... -

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Basic information

Entry
Database: PDB / ID: 6a0t
TitleHomoserine dehydrogenase K99A mutant from Thermus thermophilus HB8 complexed with HSE and NADP+
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / nad-dependent / dehydrogenase
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / NADP binding / metal ion binding
Similarity search - Function
Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, conserved site / Homoserine dehydrogenase signature. / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, conserved site / Homoserine dehydrogenase signature. / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / L-HOMOSERINE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Homoserine dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsAkai, S. / Ikushiro, H. / Sawai, T. / Yano, T. / Kamiya, N. / Miyahara, I.
CitationJournal: J. Biochem. / Year: 2019
Title: The crystal structure of homoserine dehydrogenase complexed with l-homoserine and NADPH in a closed form
Authors: Akai, S. / Ikushiro, H. / Sawai, T. / Yano, T. / Kamiya, N. / Miyahara, I.
History
DepositionJun 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Homoserine dehydrogenase
A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,97324
Polymers71,0602
Non-polymers2,91322
Water16,394910
1
A: Homoserine dehydrogenase
hetero molecules

A: Homoserine dehydrogenase
hetero molecules

B: Homoserine dehydrogenase
hetero molecules

B: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,94548
Polymers142,1194
Non-polymers5,82644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
crystal symmetry operation2_564-y,x-y+1,z-1/31
crystal symmetry operation4_565y,x+1,-z1
Buried area9470 Å2
ΔGint-29 kcal/mol
Surface area49120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.401, 121.401, 145.089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Homoserine dehydrogenase


Mass: 35529.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHA0489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SL04, homoserine dehydrogenase

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Non-polymers , 7 types, 932 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-HSE / L-HOMOSERINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / 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: 4.34 Å3/Da / Density % sol: 71.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium formate, CAPS pH 10.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 102476 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 43.4
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 7.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XDF

5xdf


Resolution: 1.87→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16664 5175 5.1 %RANDOM
Rwork0.13698 ---
obs0.13846 97192 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.758 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å2-0 Å2
2--0.14 Å20 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 188 910 6084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0195613
X-RAY DIFFRACTIONr_bond_other_d00.025432
X-RAY DIFFRACTIONr_angle_refined_deg2.5722.037674
X-RAY DIFFRACTIONr_angle_other_deg3.722312481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96122.208231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6615855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9931563
X-RAY DIFFRACTIONr_chiral_restr0.1640.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0216465
X-RAY DIFFRACTIONr_gen_planes_other0.0270.021268
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_it2.5421.9642824
X-RAY DIFFRACTIONr_mcbond_other2.5411.9652825
X-RAY DIFFRACTIONr_mcangle_it3.2682.9233581
X-RAY DIFFRACTIONr_mcangle_other3.2742.9243582
X-RAY DIFFRACTIONr_scbond_it4.3082.4512789
X-RAY DIFFRACTIONr_scbond_other4.3052.4512789
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2183.4884094
X-RAY DIFFRACTIONr_long_range_B_refined8.88919.2867200
X-RAY DIFFRACTIONr_long_range_B_other8.88819.2877200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.869→1.917 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 372 -
Rwork0.193 7113 -
obs--99.85 %

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