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- PDB-5l76: Crystal structure of human aminoadipate semialdehyde synthase, sa... -

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Basic information

Entry
Database: PDB / ID: 5l76
TitleCrystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain (in apo form)
ComponentsAlpha-aminoadipic semialdehyde synthase, mitochondrial
KeywordsOXIDOREDUCTASE / AASS / aminoadipate semialdehyde synthase / SDH
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
DI(HYDROXYETHYL)ETHER / Alpha-aminoadipic semialdehyde synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsKopec, J. / Pena, I.A. / Rembeza, E. / Strain-Damerell, C. / Chalk, R. / Borkowska, O. / Goubin, S. / Velupillai, S. / Burgess-Brown, N. / Arrowsmith, C. ...Kopec, J. / Pena, I.A. / Rembeza, E. / Strain-Damerell, C. / Chalk, R. / Borkowska, O. / Goubin, S. / Velupillai, S. / Burgess-Brown, N. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Arruda, P. / Yue, W.W.
CitationJournal: To Be Published
Title: Crystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain (in apo form)
Authors: Kopec, J. / Pena, I.A. / Rembeza, E. / Strain-Damerell, C. / Chalk, R. / Borkowska, O. / Goubin, S. / Velupillai, S. / Burgess-Brown, N. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Arruda, P. / Yue, W.W.
History
DepositionJun 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)55,0257
Polymers54,6091
Non-polymers4166
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint15 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.760, 89.760, 150.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1108-

HOH

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Components

#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 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UDR5, saccharopine dehydrogenase (NADP+, L-lysine-forming), saccharopine dehydrogenase (NAD+, L-glutamate-forming)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 -- 10% ethylene glycol -- 0.2M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.57→75.44 Å / Num. obs: 20374 / % possible obs: 99.9 % / Redundancy: 23.1 % / Biso Wilson estimate: 67.7 Å2 / CC1/2: 1 / Rsym value: 0.12 / Net I/σ(I): 22.4
Reflection shellResolution: 2.57→2.64 Å / Redundancy: 23.7 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2axq

2axq


Resolution: 2.57→63.47 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.92
RfactorNum. reflection% reflection
Rfree0.2885 757 4.76 %
Rwork0.2318 --
obs0.2344 15909 78.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.57→63.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 27 62 3346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023339
X-RAY DIFFRACTIONf_angle_d0.4894526
X-RAY DIFFRACTIONf_dihedral_angle_d10.9871996
X-RAY DIFFRACTIONf_chiral_restr0.041531
X-RAY DIFFRACTIONf_plane_restr0.003577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5702-2.76860.3432680.32051364X-RAY DIFFRACTION36
2.7686-3.04730.35281100.31812141X-RAY DIFFRACTION57
3.0473-3.48820.34211950.28653684X-RAY DIFFRACTION96
3.4882-4.39460.28321840.22273878X-RAY DIFFRACTION100
4.3946-63.48920.25122000.19534085X-RAY DIFFRACTION100

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