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- PDB-7d7p: Crystal structure of the phosphodiesterase domain of Salpingoeca ... -

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Basic information

Entry
Database: PDB / ID: 7d7p
TitleCrystal structure of the phosphodiesterase domain 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 / membrane / metal ion binding
Similarity search - Function
Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / 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. ...Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phosphodiesterase
Similarity search - Component
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8158
Polymers42,0181
Non-polymers7977
Water3,171176
1
A: Phosphodiesterase
hetero molecules

A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,63016
Polymers84,0372
Non-polymers1,59314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_559-x+1/2,y+1/2,-z+41
Unit cell
Length a, b, c (Å)117.200, 67.540, 56.890
Angle α, β, γ (deg.)90.00, 110.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1064-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphodiesterase /


Mass: 42018.496 Da / Num. of mol.: 1
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

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Non-polymers , 6 types, 183 molecules

#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 29% (v/v) PEG 400, 50mM calcium acetate, pH 5.0, 200mM NaCl

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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: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.53 Å / Num. obs: 22066 / % possible obs: 90.7 % / Redundancy: 11.6 % / CC1/2: 0.992 / Rrim(I) all: 0.162 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 1965 / CC1/2: 0.66 / Rrim(I) all: 0.798

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VYD

5vyd


Resolution: 2.1→47.516 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1101 5.01 %
Rwork0.1882 --
obs0.1907 21969 90.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 38 176 2814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022685
X-RAY DIFFRACTIONf_angle_d0.4183633
X-RAY DIFFRACTIONf_dihedral_angle_d6.0731600
X-RAY DIFFRACTIONf_chiral_restr0.034414
X-RAY DIFFRACTIONf_plane_restr0.003469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19560.29951210.23752282X-RAY DIFFRACTION80
2.1956-2.31140.28451380.20772613X-RAY DIFFRACTION91
2.3114-2.45620.2351440.19772743X-RAY DIFFRACTION95
2.4562-2.64580.26061420.19152693X-RAY DIFFRACTION94
2.6458-2.9120.28261410.18762678X-RAY DIFFRACTION93
2.912-3.33330.20941400.18662652X-RAY DIFFRACTION91
3.3333-4.19920.22811400.1732654X-RAY DIFFRACTION91
4.1992-47.5160.21811350.18172553X-RAY DIFFRACTION86

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