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- PDB-1ff9: APO SACCHAROPINE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1ff9
TitleAPO SACCHAROPINE REDUCTASE
ComponentsSACCHAROPINE REDUCTASE
KeywordsOXIDOREDUCTASE / LYSINE BIOSYNTHESIS / ALPHA-AMINOADIPATE PATHWAY / SACCHAROPINE REDUCTASE / DEHYDROGENASE
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 / Resolution: 2 Å
AuthorsJohansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Cloning, Expression, Purification and Crystallization of Saccharopine Reductase from Magnaporthe Grisea
Authors: Johansson, E. / Steffens, J.J. / Emptage, M. / Lindqvist, Y. / Schneider, G.
History
DepositionJul 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 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 / Item: _software.classification / _software.name
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 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4444
Polymers49,1561
Non-polymers2883
Water3,423190
1
A: SACCHAROPINE REDUCTASE
hetero molecules

A: SACCHAROPINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8898
Polymers98,3132
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)114.986, 56.584, 74.299
Angle α, β, γ (deg.)90.00, 111.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SACCHAROPINE REDUCTASE


Mass: 49156.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Production host: Escherichia coli (E. coli) / Strain (production host): FM5/PDB45
References: UniProt: Q9P4R4, saccharopine dehydrogenase (NAD+, L-lysine-forming)
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.8
Details: ammonium sulphate, sodium acetate, DTT, pH 4.8, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
22.5 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoir
41 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9058
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9058 Å / Relative weight: 1
ReflectionResolution: 2→24.91 Å / Num. all: 29843 / Num. obs: 578167 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.4 % / Biso Wilson estimate: 22.3 Å2 / Limit h max: 53 / Limit h min: -57 / Limit k max: 28 / Limit k min: -57 / Limit l max: 37 / Limit l min: 0 / Observed criterion F max: 1953730.55 / Observed criterion F min: 11.1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.33 / Num. unique all: 1994 / % possible all: 98.3
Reflection
*PLUS
Num. obs: 29843 / Num. measured all: 578167
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2→24.91 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1.01 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1509 5.1 %random
Rwork0.241 ---
all-30292 --
obs-29842 98.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 52.8425 Å2 / ksol: 0.347881 e/Å3
Displacement parametersBiso max: 85.56 Å2 / Biso mean: 40.66 Å2 / Biso min: 19.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å2-3.15 Å2
2--10.49 Å20 Å2
3----7.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 15 190 3628
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.6
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.29 206 5.5 %
Rwork0.288 3495 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / Rfactor Rwork: 0.288 / Rfactor obs: 0.283

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