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- PDB-7d7q: Crystal structure of the transmembrane domain and linker region o... -

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Basic information

Entry
Database: PDB / ID: 7d7q
TitleCrystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase
ComponentsPhosphodiesterase
KeywordsMEMBRANE PROTEIN / microbial rhodopsin / eight-transmembrane / light-dependent phosphodiesterase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / 3',5'-cyclic-nucleotide phosphodiesterase activity / signal transduction / metal ion binding / membrane
Similarity search - Function
Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase ...Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Phosphodiesterase
Similarity search - Component
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsIkuta, T. / Shihoya, W. / Yamashita, K. / Nureki, O.
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into the mechanism of rhodopsin phosphodiesterase.
Authors: Ikuta, T. / Shihoya, W. / Sugiura, M. / Yoshida, K. / Watari, M. / Tokano, T. / Yamashita, K. / Katayama, K. / Tsunoda, S.P. / Uchihashi, T. / Kandori, H. / Nureki, O.
History
DepositionOct 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphodiesterase
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5228
Polymers78,5272
Non-polymers1,9956
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-31 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.300, 136.530, 206.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Phosphodiesterase


Mass: 39263.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salpingoeca rosetta (strain ATCC 50818 / BSB-021) (eukaryote)
Gene: PTSG_02023 / Production host: Homo sapiens (human)
References: UniProt: F2TZN0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
Has ligand of interestN
Has protein modificationY

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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: 3.42 Å3/Da / Density % sol: 64.09 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 25% (w/v) PEG 500DME, 100mM Na-citrate, pH 5.0, 100mM NaK-tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→49.4 Å / Num. obs: 13712 / % possible obs: 98.1 % / Redundancy: 6.55 % / Biso Wilson estimate: 49.61 Å2 / CC1/2: 0.934 / Rrim(I) all: 0.673 / Net I/σ(I): 3.9
Reflection shellResolution: 3.5→3.71 Å / Num. unique obs: 2147 / CC1/2: 0.393 / Rrim(I) all: 2.868

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CJ3

7cj3


Resolution: 3.5→49.4 Å / SU ML: 0.4813 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3612
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3144 687 5.02 %
Rwork0.2663 12988 -
obs0.2686 13675 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.37 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4485 0 126 0 4611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224728
X-RAY DIFFRACTIONf_angle_d0.63516422
X-RAY DIFFRACTIONf_chiral_restr0.0358727
X-RAY DIFFRACTIONf_plane_restr0.0032796
X-RAY DIFFRACTIONf_dihedral_angle_d13.46682758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.770.3161440.31082504X-RAY DIFFRACTION97.42
3.77-4.150.34171320.27152584X-RAY DIFFRACTION98.44
4.15-4.750.30211380.25222604X-RAY DIFFRACTION98.24
4.75-5.980.31831350.27192607X-RAY DIFFRACTION98.03
5.98-49.40.30021380.24392689X-RAY DIFFRACTION96.65

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