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

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Basic information

Entry
Database: PDB / ID: 5ilg
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 / all-trans-retinol dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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
PHENOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Photoreceptor dehydrogenase, isoform C / HL08057p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)60,73011
Polymers58,9802
Non-polymers1,7509
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-61 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.195, 93.477, 114.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#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 / Plasmid: pet45 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7KNR7, UniProt: Q9VV42*PLUS, alcohol dehydrogenase, all-trans-retinol dehydrogenase (NAD+)

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, phenol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2015
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.12→114.67 Å / Num. obs: 27821 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.149 / Rsym value: 0.167 / Net I/av σ(I): 10.6 / Net I/σ(I): 14.62

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B2L
Resolution: 2.4→72.455 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 942 4.89 %RANDOM
Rwork0.1711 ---
obs0.1736 19256 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→72.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 0 116 253 4302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174117
X-RAY DIFFRACTIONf_angle_d1.3765576
X-RAY DIFFRACTIONf_dihedral_angle_d13.5391479
X-RAY DIFFRACTIONf_chiral_restr0.071654
X-RAY DIFFRACTIONf_plane_restr0.006705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52650.32091290.26512543X-RAY DIFFRACTION100
2.5265-2.68480.30181300.23172575X-RAY DIFFRACTION100
2.6848-2.89220.24531180.20722593X-RAY DIFFRACTION100
2.8922-3.18320.2741280.18952598X-RAY DIFFRACTION100
3.1832-3.64380.21311320.16652607X-RAY DIFFRACTION100
3.6438-4.59070.1891440.13582634X-RAY DIFFRACTION100
4.5907-72.48760.18781610.14652764X-RAY DIFFRACTION100

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