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- PDB-1ebf: HOMOSERINE DEHYDROGENASE FROM S. CEREVISIAE COMPLEX WITH NAD+ -

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Basic information

Entry
Database: PDB / ID: 1ebf
TitleHOMOSERINE DEHYDROGENASE FROM S. CEREVISIAE COMPLEX WITH NAD+
ComponentsHOMOSERINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / dehydrogenase / dinucleotide / homoserine / NAD / dimer
Function / homology
Function and homology information


aspartate family amino acid biosynthetic process / homoserine biosynthetic process / aspartate kinase activity / homoserine dehydrogenase / homoserine dehydrogenase activity / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homoserine dehydrogenase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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 Siffraction 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 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5375
Polymers76,8282
Non-polymers7093
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-20 kcal/mol
Surface area29700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.396, 80.396, 250.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe asymmetric unit contains a dimer with a single NAD+ molecule bound to one protomer and a sodium ion bound to each protomer

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Components

#1: Protein HOMOSERINE DEHYDROGENASE /


Mass: 38413.766 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: Ammonium sulphate, Calcium chloride, NAD+, Sodium Acetate , pH 4.4, 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: Jan 16, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→38 Å / Num. all: 36978 / Num. obs: 188533 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.49 / Num. unique all: 3445 / % possible all: 94.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 94.8 %

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Processing

Software
NameClassification
SOLVEphasing
SHARPphasing
GLRFphasing
CCP4model building
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
DMphasing
CNSphasing
RefinementResolution: 2.3→35.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 112809.29 / 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
Rfree0.269 2232 6.9 %RANDOM
Rwork0.218 ---
all0.234 35733 --
obs0.218 32162 85.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.97 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2--1.19 Å20 Å2
3----2.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5420 5717 46 253 11436
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 270 6.9 %
Rwork0.227 3642 -
obs--64.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2NAD_MOD.PARWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMNAD.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_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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