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- PDB-5ilo: Crystal structure of photoreceptor dehydrogenase from Drosophila ... -

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Basic information

Entry
Database: PDB / ID: 5ilo
TitleCrystal structure of photoreceptor dehydrogenase from Drosophila melanogaster
ComponentsPhotoreceptor dehydrogenase, isoform C
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) / retinal metabolic process / NAD-retinol dehydrogenase activity / retinol metabolic process / nucleotide binding / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / Photoreceptor dehydrogenase, isoform C / HL08057p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsHofmann, L. / Tsybovsky, Y. / Banerjee, S.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family.
Authors: Hofmann, L. / Tsybovsky, Y. / Alexander, N.S. / Babino, D. / Leung, N.Y. / Montell, C. / Banerjee, S. / von Lintig, J. / Palczewski, K.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photoreceptor dehydrogenase, isoform C
B: Photoreceptor dehydrogenase, isoform C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3074
Polymers58,9802
Non-polymers1,3272
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-51 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.159, 62.646, 114.113
Angle α, β, γ (deg.)90.00, 96.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Photoreceptor dehydrogenase, isoform C / Pigment cell dehydrogenase reductase


Mass: 29490.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Pdh, pcdr, CG4899, Dmel_CG4899 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7KNR7, UniProt: Q9VV42*PLUS, alcohol dehydrogenase, all-trans-retinol dehydrogenase (NAD+)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 121 / 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: 41.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, beta- ionone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.71→113.43 Å / Num. obs: 13342 / % possible obs: 98.5 % / Redundancy: 3.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.163 / Rsym value: 0.187 / Net I/av σ(I): 9.5 / Net I/σ(I): 9.53
Reflection shellResolution: 2.71→2.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.4 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B2L
Resolution: 2.71→113.43 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 608 4.56 %
Rwork0.2039 --
obs0.2063 13319 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→113.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 88 124 4120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034062
X-RAY DIFFRACTIONf_angle_d0.7445509
X-RAY DIFFRACTIONf_dihedral_angle_d14.0111454
X-RAY DIFFRACTIONf_chiral_restr0.03648
X-RAY DIFFRACTIONf_plane_restr0.003694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7105-2.98330.37331680.29252983X-RAY DIFFRACTION94
2.9833-3.4150.31331490.23913206X-RAY DIFFRACTION100
3.415-4.30260.24461440.19413234X-RAY DIFFRACTION100
4.3026-113.53260.19931470.1653288X-RAY DIFFRACTION100

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