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- PDB-5o1n: Crystal structure of human aminoadipate semialdehyde synthase, sa... -

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Basic information

Entry
Database: PDB / ID: 5o1n
TitleCrystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain with N-[(2S)-2-Pyrrolidinylmethyl]-trifluoromethanesulfonamide bound
ComponentsAlpha-aminoadipic semialdehyde synthase, mitochondrial
KeywordsOXIDOREDUCTASE / human aminoadipate semialdehyde synthase / saccharopine dehydrogenase domain with N-[(2S)-2-Pyrrolidinylmethyl]-trifluoromethanesulfonamide bound
Function / homology
Function and homology information


saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / lysine biosynthetic process via aminoadipic acid / Lysine catabolism ...saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / lysine biosynthetic process via aminoadipic acid / Lysine catabolism / transcription corepressor activity / histone binding / mitochondrial matrix / intracellular membrane-bounded organelle / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain ...: / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-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
Chem-9H8 / DI(HYDROXYETHYL)ETHER / Alpha-aminoadipic semialdehyde synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKopec, J. / Rembeza, E. / Pena, I.A. / Strain-Damerell, C. / Goubin, S. / Sethi, R. / Velupillai, S. / Talon, R. / Collins, P. / Krojer, T. ...Kopec, J. / Rembeza, E. / Pena, I.A. / Strain-Damerell, C. / Goubin, S. / Sethi, R. / Velupillai, S. / Talon, R. / Collins, P. / Krojer, T. / McLaughlin, M. / Burgess-Brown, N. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Brennan, P. / von Delft, F. / Arruda, P. / Yue, W.W.
CitationJournal: To Be Published
Title: Crystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain with N-[(2S)-2-Pyrrolidinylmethyl]-trifluoromethanesulfonamide bound
Authors: Kopec, J. / Yue, W.W.
History
DepositionMay 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0875
Polymers54,6091
Non-polymers4794
Water45025
1
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules

A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,17510
Polymers109,2182
Non-polymers9578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_467y-1,x+1,-z+21
Buried area3400 Å2
ΔGint7 kcal/mol
Surface area35860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.396, 89.396, 147.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-aminoadipic semialdehyde synthase, mitochondrial / LKR/SDH


Mass: 54608.812 Da / Num. of mol.: 1 / Fragment: UNP residues 455-926
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AASS / Plasmid: pFB-LIC-Bse / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UDR5, saccharopine dehydrogenase (NADP+, L-lysine-forming), saccharopine dehydrogenase (NAD+, L-glutamate-forming)

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Non-polymers , 5 types, 29 molecules

#2: Chemical ChemComp-9H8 / 1,1,1-tris(fluoranyl)-~{N}-[[(2~{S})-pyrrolidin-2-yl]methyl]methanesulfonamide


Mass: 232.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11F3N2O2S
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.22 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG3350 -- 0.3M sodium malonate -- 0.1M tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.28→44.7 Å / Num. obs: 28144 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 55.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.9
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2038 / CC1/2: 0.758 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5l76

5l76


Resolution: 2.28→44.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.463 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.236 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28559 1371 4.9 %RANDOM
Rwork0.26483 ---
obs0.26585 26469 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.328 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å2-0 Å2-0 Å2
2--2.58 Å2-0 Å2
3----5.16 Å2
Refinement stepCycle: 1 / Resolution: 2.28→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 29 25 3338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193373
X-RAY DIFFRACTIONr_bond_other_d0.0010.023257
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.994577
X-RAY DIFFRACTIONr_angle_other_deg0.8352.9957504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8335440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17625.169118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16815557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.686159
X-RAY DIFFRACTIONr_chiral_restr0.0550.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2257.0441766
X-RAY DIFFRACTIONr_mcbond_other1.2257.0411765
X-RAY DIFFRACTIONr_mcangle_it2.20910.5582204
X-RAY DIFFRACTIONr_mcangle_other2.20910.562205
X-RAY DIFFRACTIONr_scbond_it0.9386.9821606
X-RAY DIFFRACTIONr_scbond_other0.9356.9821606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.68410.4682374
X-RAY DIFFRACTIONr_long_range_B_refined3.49254.3033522
X-RAY DIFFRACTIONr_long_range_B_other3.49254.3133523
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 97 -
Rwork0.45 1887 -
obs--97.78 %

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