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- PDB-1ebu: HOMOSERINE DEHYDROGENASE COMPLEX WITH NAD ANALOGUE AND L-HOMOSERINE -

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Basic information

Entry
Database: PDB / ID: 1ebu
TitleHOMOSERINE DEHYDROGENASE COMPLEX WITH NAD ANALOGUE AND L-HOMOSERINE
ComponentsHOMOSERINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / homoserine / dehydrogenase / dinucleotide / ternary / analogue
Function / homology
Function and homology information


aspartate family amino acid biosynthetic process / aspartate kinase activity / homoserine dehydrogenase / homoserine dehydrogenase activity / homoserine biosynthetic process / threonine biosynthetic process / methionine biosynthetic process / isoleucine biosynthetic process / NADP binding / nucleus / cytoplasm
Similarity search - Function
Bifunctional aspartokinase/homoserine dehydrogenase I / 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 ...Bifunctional aspartokinase/homoserine dehydrogenase I / 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
L-HOMOSERINE / 3-AMINOMETHYL-PYRIDINIUM-ADENINE-DINUCLEOTIDE / Homoserine dehydrogenase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsDeLaBarre, B. / Thompson, P.R. / Wright, G.D. / Berghuis, A.M.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases.
Authors: DeLaBarre, B. / Thompson, P.R. / Wright, G.D. / Berghuis, A.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray diffraction studies of homoserine dehydrogenase from Saccharomyces cerevisiae
Authors: DeLaBarre, B. / Jacques, S.L. / Pratt, C.E. / Wright, G.D. / Berghuis, A.M.
History
DepositionJan 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: HOMOSERINE DEHYDROGENASE
B: HOMOSERINE DEHYDROGENASE
C: HOMOSERINE DEHYDROGENASE
D: HOMOSERINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,51610
Polymers153,6554
Non-polymers8616
Water6,323351
1
A: HOMOSERINE DEHYDROGENASE
B: HOMOSERINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8744
Polymers76,8282
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-12 kcal/mol
Surface area29260 Å2
MethodPISA
2
C: HOMOSERINE DEHYDROGENASE
D: HOMOSERINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6426
Polymers76,8282
Non-polymers8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-15 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.780, 104.090, 120.640
Angle α, β, γ (deg.)90.00, 91.93, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains 2 dimers: A/B and C/D. The ternary complex is found in the D chain protomer

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Components

#1: Protein
HOMOSERINE DEHYDROGENASE


Mass: 38413.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HOM6P / Production host: Escherichia coli (E. coli) / References: UniProt: P31116, homoserine dehydrogenase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NDA / 3-AMINOMETHYL-PYRIDINIUM-ADENINE-DINUCLEOTIDE


Mass: 649.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O13P2
#4: Chemical ChemComp-HSE / L-HOMOSERINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8K, L-homoserine, 3-aminopyridine dinucleotide, sodium cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1dropor 10 mM HEPES
320 mM1dropCaCl2
42.0 Mammonium sulfate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 218 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 22, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 44409 / Num. obs: 164716 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.344 / Num. unique all: 4392 / % possible all: 98.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.6→39.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1625863.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Model refined against amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3998 9.1 %RANDOM
Rwork0.215 ---
all0.217 44409 --
obs0.215 44116 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å28.79 Å2
2--0.66 Å20 Å2
3----2.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10840 956 55 352 12203
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.051.5
X-RAY DIFFRACTIONc_mcangle_it5.832
X-RAY DIFFRACTIONc_scbond_it6.432
X-RAY DIFFRACTIONc_scangle_it8.062.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 659 9.1 %
Rwork0.3 6567 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2NDA_HSE.PARWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMNDA_HSE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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