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- PDB-5xdf: Homoserine dehydrogenase from Thermus thermophilus HB8 complexed ... -

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Basic information

Entry
Database: PDB / ID: 5xdf
TitleHomoserine dehydrogenase from Thermus thermophilus HB8 complexed with HSE
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / nad-dependent / dehydrogenase
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / L-threonine 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 / Homoserine dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsAkai, S. / Miyahara, I.
CitationJournal: To Be Published
Title: Crystallographic study of homoserine dehydrogenase from Thermus thermophilus HB8
Authors: Akai, S. / Ikushiro, H. / Sawai, D. / Hayashi, H. / Kamiya, N. / Miyahara, I.
History
DepositionMar 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,4368
Polymers71,0602
Non-polymers3766
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-13 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.625, 119.625, 145.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SL04, homoserine dehydrogenase
#2: Chemical ChemComp-HSE / L-HOMOSERINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 4.22 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: Sodium formate, CAPS pH 10.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 80859 / % possible obs: 99.8 % / Redundancy: 11 % / Net I/σ(I): 42
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 5.7 / Num. unique obs: 4013 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0135 / Classification: refinement
RefinementResolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.024 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21913 4042 5 %RANDOM
Rwork0.18461 ---
obs0.18634 76592 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.182 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 24 499 5296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0194949
X-RAY DIFFRACTIONr_bond_other_d0.0020.024818
X-RAY DIFFRACTIONr_angle_refined_deg2.1372.0046751
X-RAY DIFFRACTIONr_angle_other_deg1.162311039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30423.048187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56615728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6481539
X-RAY DIFFRACTIONr_chiral_restr0.1510.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215674
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021057
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_it3.4082.9532633
X-RAY DIFFRACTIONr_mcbond_other3.4072.9542634
X-RAY DIFFRACTIONr_mcangle_it4.3154.3983293
X-RAY DIFFRACTIONr_mcangle_other4.3154.43294
X-RAY DIFFRACTIONr_scbond_it4.113.2972316
X-RAY DIFFRACTIONr_scbond_other4.1083.2942312
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8184.8013459
X-RAY DIFFRACTIONr_long_range_B_refined7.28324.6785730
X-RAY DIFFRACTIONr_long_range_B_other7.28124.6145713
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 296 -
Rwork0.241 5550 -
obs--99.4 %

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