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- PDB-1e5q: Ternary complex of saccharopine reductase from Magnaporthe grisea... -

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Basic information

Entry
Database: PDB / ID: 1e5q
TitleTernary complex of saccharopine reductase from Magnaporthe grisea, NADPH and saccharopine
ComponentsSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]
KeywordsOXIDOREDUCTASE / SACCHAROPINE REDUCTASE / NADPH / 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
Chem-NDP / N-(5-AMINO-5-CARBOXYPENTYL)GLUTAMIC ACID / Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJohansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G.
CitationJournal: 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.
History
DepositionJul 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description ..._diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
B: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
C: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
D: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
E: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
F: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
G: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
H: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,42424
Polymers393,2508
Non-polymers8,17416
Water45,2002509
1
A: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
B: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3566
Polymers98,3132
Non-polymers2,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
D: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3566
Polymers98,3132
Non-polymers2,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
F: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3566
Polymers98,3132
Non-polymers2,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
H: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3566
Polymers98,3132
Non-polymers2,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.643, 205.809, 125.599
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.65256, -0.64454, 0.39841), (-0.66442, 0.23394, -0.7098), (0.36429, -0.7279, -0.58091)16.2141, 79.93341, 122.33724
2given(-0.65291, -0.64359, 0.39937), (0.67739, -0.26023, 0.68806), (-0.3389, 0.71977, 0.60587)59.04107, 42.97766, -1.46661
3given(0.99997, 0.00643, 0.00486), (0.00634, -0.99984, 0.01668), (0.00497, -0.01664, -0.99985)42.41738, 119.46846, 123.22049
4given(-0.64664, -0.65014, 0.39897), (0.67234, -0.23872, 0.70069), (-0.3603, 0.72134, 0.59149)4.93305, -38.29884, 62.16428
5given(0.99997, 0.005, -0.00504), (0.00499, -0.99999, -0.00182), (-0.00505, 0.00179, -0.99999)-11.13299, 40.98387, 184.70789
6given(1, -0.00029, -0.003), (0.00029, 1, 0.00107), (0.003, -0.00107, 0.99999)54.21876, 126.08662, -61.24036
7given(-0.64883, -0.64662, 0.40113), (-0.66685, 0.22926, -0.70905), (0.36653, -0.72754, -0.57995)70.05755, 206.20409, 61.11735

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Components

#1: Protein
Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] / Saccharopine reductase


Mass: 49156.262 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: LYS3, MGG_08564 / Plasmid: PDB45 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FM5/PDB45
References: UniProt: Q9P4R4, saccharopine dehydrogenase (NADP+, L-glutamate-forming)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-SHR / N-(5-AMINO-5-CARBOXYPENTYL)GLUTAMIC ACID


Type: L-peptide linking / Mass: 276.286 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H20N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2509 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.25
Details: 8 MG/ML PROTEIN, 1 MM SACCHAROPINE, 1 MM NADPH, 20 % (W/W) PEG8000, 0.1 M TRIS-HCL PH 7.25, 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
21 mMNADPH1drop
39 mMsaccharopine1drop
420 %(w/w)PEG80001reservoir
50.1 MTris-HCl1reservoir
61 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8424 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 250975 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 18
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.5 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 2072876
Reflection shell
*PLUS
% possible obs: 96.5 %

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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: 2.1→19.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3423402.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 12322 4.9 %RANDOM
Rwork0.207 ---
obs0.207 250248 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4148 Å2 / ksol: 0.335216 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å20 Å23.69 Å2
2---4.22 Å20 Å2
3---8.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27528 0 536 2509 30573
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
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 2012 4.9 %
Rwork0.257 39135 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2XDICT_8089.PARWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE_TEST.PARAMSAC_TOP.TXT
X-RAY DIFFRACTION4SAC_PAR.TXTXDICT_8089.TOP
X-RAY DIFFRACTION5WATER_REP.PARAM
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
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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