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- PDB-2axq: Apo histidine-tagged saccharopine dehydrogenase (L-Glu forming) f... -

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Basic information

Entry
Database: PDB / ID: 2axq
TitleApo histidine-tagged saccharopine dehydrogenase (L-Glu forming) from Saccharomyces cerevisiae
ComponentsSaccharopine dehydrogenase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD VARIANT / SACCHAROPINE REDUCTASE FOLD (DOMAIN II) / ALPHA/BETA PROTEIN / ALPHA-AMINOADIPATE PATHWAY / FUNGAL LYSINE BIOSYNTHESIS
Function / homology
Function and homology information


Lysine catabolism / saccharopine dehydrogenase (NADP+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / lysine biosynthetic process via aminoadipic acid / cell periphery / cytoplasm
Similarity search - Function
Domain 3, Saccharopine reductase / Domain 3, Saccharopine reductase / : / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Domain 3, Saccharopine reductase / Domain 3, Saccharopine reductase / : / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAndi, B. / Cook, P.F. / West, A.H.
Citation
Journal: Cell Biochem.Biophys. / Year: 2006
Title: Crystal structure of the his-tagged saccharopine reductase from Saccharomyces cerevisiae at 1.7-A resolution.
Authors: Andi, B. / Cook, P.F. / West, A.H.
#1: Journal: Structure Fold.Des. / Year: 2000
Title: Crystal Structure of Saccharopine Reductase from Magnaporthe Grisea, an Enzyme of the Alpha-Aminoadipate Pathway of Lysine Biosynthesis
Authors: Johansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G.
History
DepositionSep 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Saccharopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8905
Polymers51,5051
Non-polymers3844
Water6,287349
1
A: Saccharopine dehydrogenase
hetero molecules

A: Saccharopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,77910
Polymers103,0112
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Unit cell
Length a, b, c (Å)85.279, 85.279, 141.977
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

DetailsThe biological assembly is a homodimer generated from the monomer in the asymmetric unit by the operations: y, x, -z

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Components

#1: Protein Saccharopine dehydrogenase / Saccharopine reductase


Mass: 51505.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: L-Glu forming
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LYS9, LYS13 / Plasmid: pET-16b-LYS9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star(DE3)-RIL
References: UniProt: P38999, saccharopine dehydrogenase (NADP+, L-glutamate-forming)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.9 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.2M Ammonium sulfate, 25mM Bis-Tris, 6.5-7mg/mL enzyme, 50mM Tris-HCl pH 8.0, 150mM KCl, 75mM imidazole, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 18, 2003 / Details: MICRO-OPTICS
RadiationMonochromator: OSMIC CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→39.85 Å / Num. all: 66370 / Num. obs: 64775 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.18 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1 / Net I/σ(I): 15.8 / Scaling rejects: 3516
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 95.9 % / Redundancy: 4.98 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 324 / Num. unique all: 6559 / Χ2: 1.16 / % possible all: 95.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å8 Å
Translation3 Å8 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2Ddata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
CrystalClearD*TREK (MSC/RIGAKU)data reduction
CCP4(TRUNCATE)data scaling
ARP/wARPmodel building
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E5L, used monomer, backbone only

1e5l


Resolution: 1.7→39.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.661 / SU ML: 0.084 / Isotropic thermal model: Mixed (isotropic/anisotropic) / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.099 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The first methionine residue and N-terminal deca-histidine tag could not be built because of missing electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3290 5.1 %RANDOM
Rwork0.198 ---
all0.2 64787 --
obs0.2 64774 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.219 Å
Refinement stepCycle: LAST / Resolution: 1.7→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 20 349 3813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223532
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9844799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54224.615143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15815604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7051516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022624
X-RAY DIFFRACTIONr_nbd_refined0.2070.21660
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2337
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.216
X-RAY DIFFRACTIONr_mcbond_it2.50642289
X-RAY DIFFRACTIONr_mcangle_it3.40953578
X-RAY DIFFRACTIONr_scbond_it2.70941443
X-RAY DIFFRACTIONr_scangle_it3.48341221
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 261 -
Rwork0.312 4383 -
all-4644 -
obs--95.4 %

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