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- PDB-2q99: Crystal Structure of Saccharopine Dehydrogenase from Saccharomyce... -

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Basic information

Entry
Database: PDB / ID: 2q99
TitleCrystal Structure of Saccharopine Dehydrogenase from Saccharomyces cerevisiae
ComponentsSaccharopine dehydrogenase [NAD+, L-lysine-forming
KeywordsOXIDOREDUCTASE / dehydrogenase / alpha-aminoadipate pathway / fungal lysine synthesis / alpha/beta protein / Rossmann fold
Function / homology
Function and homology information


saccharopine dehydrogenase (NAD+, L-lysine-forming) / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine biosynthetic process / protein import into peroxisome matrix / lysine biosynthetic process via aminoadipic acid / peroxisome / mRNA binding / cytoplasm
Similarity search - Function
Saccharopine dehydrogenase [NAD(+), L-lysine-forming] / : / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Saccharopine dehydrogenase [NAD(+), L-lysine-forming] / : / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Saccharopine dehydrogenase [NAD(+), L-lysine-forming]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å
AuthorsBerghuis, A.M. / Burk, D.L.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Studies of the Final Enzyme in the alpha-Aminoadipate Pathway-Saccharopine Dehydrogenase from Saccharomyces cerevisiae
Authors: Burk, D.L. / Hwang, J. / Kwok, E. / Marrone, L. / Goodfellow, V. / Dmitrienko, G.I. / Berghuis, A.M.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Saccharopine dehydrogenase [NAD+, L-lysine-forming


Theoretical massNumber of molelcules
Total (without water)42,3171
Polymers42,3171
Non-polymers00
Water9,710539
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.680, 74.920, 74.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the monomer observed in the asymmetric unit.

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Components

#1: Protein Saccharopine dehydrogenase [NAD+, L-lysine-forming / Lysine--2-oxoglutarate reductase / SDH


Mass: 42317.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LYS1 / Plasmid: pGEX-6T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P38998, saccharopine dehydrogenase (NAD+, L-lysine-forming)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 8000, 0.2 M calcium acetate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9200,0.9794,0.9796,1.0080
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.97941
30.97961
41.0081
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
13.61105579310.0761.11.74092399.9
6.7211.33010730.0731.141.644494698.8
13.9310.55656840.0691.071.74061499.9
6.7411.82761250.0551.091.694147399.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665099.410.0461.80613.2
2.913.6610010.0491.22914
2.542.9110010.0671.12414.1
2.312.5410010.0881.05714.1
2.142.3110010.1241.08714
2.022.1410010.1761.06113.8
1.912.0210010.2381.00213.6
1.831.9110010.3560.90613.5
1.761.8310010.5050.83913.4
1.71.7699.910.6610.79712.7
3.535099.420.0481.326.6
2.83.5310020.0480.9497
2.452.810020.0681.0347.1
2.232.4510020.0921.2277
2.072.2310020.1321.2567
1.942.0710020.1871.2026.9
1.851.9499.820.2851.2596.8
1.771.8599.620.4191.0716.7
1.71.7799.520.5881.0376.5
1.641.789.320.6991.0115.2
3.665099.430.0391.21313.5
2.913.6610030.0431.02514.3
2.542.9110030.061.01414.4
2.312.5410030.0811.03314.5
2.142.3110030.1161.12614.3
2.022.1410030.1671.17614
1.912.0210030.2271.12313.8
1.831.9110030.3381.06413.6
1.761.8310030.4780.97613.5
1.71.7610030.6350.91713.4
3.645098.740.0321.1036.5
2.893.6410040.0340.9776.9
2.522.8910040.0491.0087
2.292.5210040.0681.0757
2.132.2910040.1051.2526.9
22.1310040.1461.2396.8
1.9210040.2041.2066.7
1.821.999.940.2951.0616.7
1.751.8299.840.4180.9646.5
1.691.7598.740.5270.9595.3
ReflectionResolution: 1.64→48.97 Å / Num. all: 44888 / Num. obs: 44946 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 23.8 Å2 / Limit h max: 39 / Limit h min: 0 / Limit k max: 45 / Limit k min: 0 / Limit l max: 45 / Limit l min: 0 / Observed criterion F max: 285622.8 / Observed criterion F min: 0.16 / Rmerge(I) obs: 0.073 / Χ2: 1.141 / Net I/σ(I): 11.3
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.699 / Num. unique all: 4015 / Χ2: 1.011 / % possible all: 89.3

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
4
Phasing MADD res high: 1.7 Å / D res low: 20 Å / FOM : 0.45 / Reflection: 40357
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
14 wavelength10.97956.6-9.18
14 wavelength20.97966.45-10.53
14 wavelength30.923.77-3.56
14 wavelength41.0080.55-3.34
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se20.1360.2110.5580.2420.493
2Se38.8060.9270.1620.1120.597
3Se25.1640.3960.80.1160.535
Phasing MAD shell
Resolution (Å)FOM Reflection
6.02-200.772073
3.83-6.020.713443
3.01-3.830.74316
2.55-3.010.645057
2.26-2.550.515654
2.05-2.260.386255
1.88-2.050.266623
1.75-1.880.156936
Phasing dmFOM : 0.6 / FOM acentric: 0.6 / FOM centric: 0.63 / Reflection: 40358 / Reflection acentric: 36467 / Reflection centric: 3891
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.9-19.8160.960.970.9418871426461
3-4.90.940.950.955474764783
2.4-30.840.860.7668716163708
2.1-2.40.690.70.668536253600
1.8-2.10.440.450.381199611100896
1.7-1.80.210.210.1872046761443

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
CNS1.2refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.64→48.97 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 285436.719 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CROSS-VALIDATION METHOD: "THROUGHOUT" FREE R VALUE TEST SET SELECTION CRITERIA: "RANDOM" NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. POLYMER 3016 NONPOLYMER 0 SOLVENT 556
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2182 5 %RANDOM
Rwork0.187 ---
all-45052 --
obs-43760 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.488 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 69.79 Å2 / Biso mean: 25 Å2 / Biso min: 10.49 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å20 Å20 Å2
2---4.84 Å20 Å2
3---8.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Luzzati d res high-1.64
Refinement stepCycle: LAST / Resolution: 1.64→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 0 539 3555
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg22.8
X-RAY DIFFRACTIONc_torsion_impr_deg0.8
X-RAY DIFFRACTIONc_mcbond_it2.281.5
X-RAY DIFFRACTIONc_mcangle_it3.062
X-RAY DIFFRACTIONc_scbond_it3.892
X-RAY DIFFRACTIONc_scangle_it5.232.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.64-1.720.3412494.90.34348350.0225569508491.3
1.72-1.810.2992735.20.27949580.0185547523194.3
1.81-1.920.322735.10.24350900.0195580536396.1
1.92-2.070.24527350.251880.0155596546197.6
2.07-2.280.2272684.90.18652390.0145590550798.5
2.28-2.610.20128150.17353110.0125636559299.2
2.61-3.290.2212804.90.1853860.0135687566699.6
3.29-48.970.1742854.90.16655710.015895585699.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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