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- PDB-3abi: Crystal Structure of L-Lysine Dehydrogenase from Hyperthermophili... -

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Basic information

Entry
Database: PDB / ID: 3abi
TitleCrystal Structure of L-Lysine Dehydrogenase from Hyperthermophilic Archaeon Pyrococcus horikoshii
ComponentsPutative uncharacterized protein PH1688
KeywordsOXIDOREDUCTASE / L-LYSINE DEHYDROGENASE / PYROCOCCUS HORIKOSHII
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / 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 ...: / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Saccharopine dehydrogenase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.44 Å
AuthorsYoneda, K. / Sakuraba, H. / Fukuda, J. / Ohshima, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: First crystal structure of L-lysine 6-dehydrogenase as an NAD-dependent amine dehydrogenase.
Authors: Yoneda, K. / Fukuda, J. / Sakuraba, H. / Ohshima, T.
History
DepositionDec 14, 2009Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 29, 2009ID: 3A63
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative uncharacterized protein PH1688
B: Putative uncharacterized protein PH1688
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1316
Polymers83,6122
Non-polymers1,5194
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-16 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.291, 113.011, 122.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein PH1688 / L-lysine dehydrogenase


Mass: 41806.234 Da / Num. of mol.: 2 / Fragment: UNP residues 4-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1688 / Plasmid: PCOLD I / Production host: Escherichia coli (E. coli) / References: UniProt: O59312, EC: 1.4.1.18
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 2.1M AMMONIUM SULFATE, 0.1M CITRATE BUFFER, PH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.99321, 1.00900, 0.99284, 1.00
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.993211
21.0091
30.992841
411
ReflectionResolution: 2.44→83.045 Å / Num. obs: 39442 / Biso Wilson estimate: 35.7 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.44→47.51 Å
RfactorNum. reflection
Rfree0.2355 -
Rwork0.2245 -
obs-39363
Refinement stepCycle: LAST / Resolution: 2.44→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5563 0 98 135 5796

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