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- PDB-1sny: Carbonyl reductase Sniffer of D. melanogaster -

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Basic information

Entry
Database: PDB / ID: 1sny
TitleCarbonyl reductase Sniffer of D. melanogaster
Componentssniffer CG10964-PA
KeywordsOXIDOREDUCTASE / alpha and beta protein / Rossmann fold / dinucleotide binding motif
Function / homology
Function and homology information


carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / : / nucleotide binding
Similarity search - Function
short chain dehydrogenase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / LD36273p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsSgraja, T. / Ulschmid, J. / Becker, K. / Schneuwly, S. / Klebe, G. / Reuter, K. / Heine, A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural Insights into the Neuroprotective-acting Carbonyl Reductase Sniffer of Drosophila melanogaster.
Authors: Sgraja, T. / Ulschmid, J. / Becker, K. / Schneuwly, S. / Klebe, G. / Reuter, K. / Heine, A.
History
DepositionMar 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sniffer CG10964-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7842
Polymers29,0401
Non-polymers7431
Water1,02757
1
A: sniffer CG10964-PA
hetero molecules

A: sniffer CG10964-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5674
Polymers58,0802
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area6090 Å2
ΔGint-40 kcal/mol
Surface area18980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.700, 73.900, 92.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein sniffer CG10964-PA


Mass: 29040.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sniffer / Plasmid: pQE16 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (Qiagen) / References: UniProt: Q9W3H4
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, sodium acetate, tris hydrogen chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.980163, 0.979944, 0.932328
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 22, 2003 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9801631
20.9799441
30.9323281
ReflectionResolution: 1.75→28.84 Å / Num. obs: 24381 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 22.7
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.1 / Num. unique all: 24381 / Rsym value: 0.498 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
SHELXLrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.75→28.84 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1209442.33 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: poorly defined sections in the structure: amino acid 10 to 18, 22 to 26 and 37 to 53
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1079 5 %RANDOM
Rwork0.247 ---
obs0.247 21565 85.9 %-
all-21565 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.8512 Å2 / ksol: 0.376692 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.04 Å20 Å20 Å2
2--16.84 Å20 Å2
3----10.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.75→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 48 57 1952
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 123 4.5 %
Rwork0.349 2621 -
obs-2621 66.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIG.PARLIG.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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