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- PDB-1iy8: Crystal Structure of Levodione Reductase -

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Basic information

Entry
Database: PDB / ID: 1iy8
TitleCrystal Structure of Levodione Reductase
ComponentsLEVODIONE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Levodione reductase
Similarity search - Component
Biological speciesLeifsonia aquatica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSogabe, S. / Fukami, T. / Shiratori, Y. / Yoshizumi, A. / Wada, M.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: The Crystal Structure and Stereospecificity of Levodione Reductase from Corynebacterium aquaticum M-13
Authors: Sogabe, S. / Yoshizumi, A. / Fukami, T. / Shiratori, Y. / Shimizu, S. / Takagi, H. / Nakamori, S. / Wada, M.
History
DepositionJul 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: LEVODIONE REDUCTASE
B: LEVODIONE REDUCTASE
C: LEVODIONE REDUCTASE
D: LEVODIONE REDUCTASE
E: LEVODIONE REDUCTASE
F: LEVODIONE REDUCTASE
G: LEVODIONE REDUCTASE
H: LEVODIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,81524
Polymers223,5628
Non-polymers6,25316
Water17,186954
1
A: LEVODIONE REDUCTASE
B: LEVODIONE REDUCTASE
C: LEVODIONE REDUCTASE
D: LEVODIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,90812
Polymers111,7814
Non-polymers3,1268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20300 Å2
ΔGint-90 kcal/mol
Surface area30980 Å2
MethodPISA
2
E: LEVODIONE REDUCTASE
F: LEVODIONE REDUCTASE
G: LEVODIONE REDUCTASE
H: LEVODIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,90812
Polymers111,7814
Non-polymers3,1268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20230 Å2
ΔGint-88 kcal/mol
Surface area30810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.672, 79.184, 112.670
Angle α, β, γ (deg.)103.87, 91.40, 105.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
LEVODIONE REDUCTASE


Mass: 27945.305 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leifsonia aquatica (bacteria) / Strain: M-13 / Plasmid: pkk223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LBG2
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 954 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG MME 2000, magnesium chloride, MPD, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
218-20 %(w/v)PEG2000 MME1reservoir
30.2 M1reservoirMgCl2
45 %(v/v)MPD1reservoir
55 %(v/v)glycerol1reservoir
60.1 MMES1reservoirpH6.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL24XU10.836
SYNCHROTRONSPring-8 BL38B121
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEJan 24, 2002
ADSC QUANTUM 42CCDDec 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8361
211
ReflectionResolution: 1.6→40 Å / Num. obs: 261092 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.7 Å / % possible all: 83.2
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 92.1 % / Redundancy: 4 % / Num. measured all: 1031771 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 82.7 % / Rmerge(I) obs: 0.263

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HSD

2hsd


Resolution: 1.6→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.219 13162 RAMDOM
Rwork0.199 --
obs-261092 -
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15232 0 352 1018 16602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.53
Refinement
*PLUS
Num. reflection obs: 16602 / % reflection Rfree: 5 % / Rfactor Rfree: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.534
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.254

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