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- PDB-6a0r: Homoserine dehydrogenase from Thermus thermophilus HB8 unliganded form -

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Basic information

Entry
Database: PDB / ID: 6a0r
TitleHomoserine dehydrogenase from Thermus thermophilus HB8 unliganded form
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / nad-dependent / dehydrogenase
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / isoleucine 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 / Unknown ligand / Homoserine dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 1.2Nov 22, 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
B: Homoserine dehydrogenase
A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,69326
Polymers71,0602
Non-polymers1,63324
Water13,673759
1
B: Homoserine dehydrogenase
hetero molecules

B: Homoserine dehydrogenase
hetero molecules

A: Homoserine dehydrogenase
hetero molecules

A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,38652
Polymers142,1194
Non-polymers3,26748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
crystal symmetry operation3_455-x+y-1,-x,z+1/31
crystal symmetry operation4_455y-1,x,-z1
Buried area16680 Å2
ΔGint-34 kcal/mol
Surface area48180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.197, 119.197, 144.547
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 , 6 types, 783 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 178.228 Da / Num. of mol.: 1 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAuthors state that they do not use 4-~{tert}-butylbenzoic acid or the derivatives as a ...Authors state that they do not use 4-~{tert}-butylbenzoic acid or the derivatives as a crystallization solution. Therefore, even though the electron density map is clearly 4-~{tert}-butylbenzoic acid, the ligand is assigned to 'unknown ligand (UNL)'

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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: 4.17 Å3/Da / Density % sol: 70.51 %
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: Jun 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 104929 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 48.7
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 7 / % 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: 1.83→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17707 5231 5 %RANDOM
Rwork0.14825 ---
obs0.14971 99528 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 106 759 5849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0195484
X-RAY DIFFRACTIONr_bond_other_d00.025369
X-RAY DIFFRACTIONr_angle_refined_deg2.5142.0127465
X-RAY DIFFRACTIONr_angle_other_deg3.724312341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.535720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32222.522230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94815855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.021559
X-RAY DIFFRACTIONr_chiral_restr0.1740.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0216347
X-RAY DIFFRACTIONr_gen_planes_other0.0260.021224
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_it3.3952.4412793
X-RAY DIFFRACTIONr_mcbond_other3.3942.4412794
X-RAY DIFFRACTIONr_mcangle_it4.3653.6353530
X-RAY DIFFRACTIONr_mcangle_other4.3653.6383531
X-RAY DIFFRACTIONr_scbond_it4.6972.9482691
X-RAY DIFFRACTIONr_scbond_other4.6972.9472690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8474.2243932
X-RAY DIFFRACTIONr_long_range_B_refined9.22222.386746
X-RAY DIFFRACTIONr_long_range_B_other9.22122.386747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.829→1.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 378 -
Rwork0.207 7229 -
obs--99.79 %

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