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- PDB-1e5l: Apo saccharopine reductase from Magnaporthe grisea -

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Basic information

Entry
Database: PDB / ID: 1e5l
TitleApo saccharopine reductase from Magnaporthe grisea
ComponentsSACCHAROPINE REDUCTASE
KeywordsOXIDOREDUCTASE / SACCHAROPINE REDUCTASE / LYSINE BIOSYNTHESIS / ALPHA- AMINOADIPATE PATHWAY
Function / homology
Function and homology information


saccharopine dehydrogenase (NADP+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity / lysine biosynthetic process via aminoadipic acid / 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 speciesMAGNAPORTHE GRISEA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJohansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G.
Citation
Journal: Structure / 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Cloning, Expression, Purification and Crystallization of Saccharopine Reductase from Magnaporthe Grisea, an Enzyme of the Alpha-Aminoadipate Pathway of Lysine Biosynthesis
Authors: Johansson, E. / Steffens, J.J. / Emptage, M. / Lindqvist, Y. / Schneider, G.
History
DepositionJul 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SACCHAROPINE REDUCTASE
B: SACCHAROPINE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)98,3132
Polymers98,3132
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.330, 119.000, 195.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.56243, 0.35127, 0.74852), (0.33769, -0.72875, 0.59573), (0.75474, 0.58783, 0.29125)
Vector: 8.62276, -27.46522, 34.30939)

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Components

#1: Protein SACCHAROPINE REDUCTASE / SACCHAROPNE DEHYDROGENASE (GLUTAMATE FORMING) / ALPHA-AMINOADIPATE-DELTA-SEMIALDEHYDE-GLUTAMATE REDUCTASE


Mass: 49156.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MAGNAPORTHE GRISEA (fungus) / Gene: LYS3 / Plasmid: PDB45 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FM5/PDB45
References: UniProt: Q9P4R4*PLUS, saccharopine dehydrogenase (NADP+, L-glutamate-forming)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDESCRIBED IN JOHANSSON ET AL.(2000) ACTA CRYST. D56 662-664

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 4
Details: 8 MG/ML PROTEIN, 11-14 % (W/W) PEG6000, 0.1 M CITRIC ACID PH 4.0, 0.1 % BETA-OCTYLGLUCOSIDE, 1 MM DTT
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
20.5 %beta-octylglucoside1drop
311-14 %(w/w)PEG60001reservoir
40.1 Mcitric acid1reservoir
51 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.104
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.104 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 40017 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.3 / % possible all: 82.2
Reflection
*PLUS
Num. measured all: 386685 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 82.2 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF9

1ff9


Resolution: 2.4→19.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2970901.79 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: MLF REFINEMENT TARGET
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1961 4.9 %RANDOM
Rwork0.222 ---
obs0.222 39933 97.1 %-
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.54 Å20 Å20 Å2
2---3.01 Å20 Å2
3----5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6884 0 0 171 7055
Refine LS restraints
Refine-IDTypeDev ideal
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_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 310 5.1 %
Rwork0.274 5804 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / 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_deg0.83
LS refinement shell
*PLUS
Rfactor obs: 0.274

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