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- PDB-7w74: Crystal structure of DTG rhodopsin from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 7w74
TitleCrystal structure of DTG rhodopsin from Pseudomonas putida
ComponentsBacteriorhodopsin-like protein
KeywordsMEMBRANE PROTEIN / light-driven proton pump / seven transmembrane helices / retinal / DTG motif
Function / homology
Function and homology information


: / monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane => GO:0016020
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin-like protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsSuzuki, K. / Konno, M. / Bagherzadeh, R. / Inoue, K. / Murata, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography.
Authors: Suzuki, K. / Del Carmen Marin, M. / Konno, M. / Bagherzadeh, R. / Murata, T. / Inoue, K.
History
DepositionDec 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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: Bacteriorhodopsin-like protein
B: Bacteriorhodopsin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,07011
Polymers52,0052
Non-polymers3,0659
Water30617
1
A: Bacteriorhodopsin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0707
Polymers26,0031
Non-polymers2,0676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0004
Polymers26,0031
Non-polymers9983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.565, 65.565, 219.363
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Bacteriorhodopsin-like protein / DTG rhodopsin


Mass: 26002.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: F633_03659 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A370SAH7
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 296 K / Method: lipidic cubic phase / pH: 4
Details: Magnesium chloride, Sodium chloride, Sodium citrate, PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.84→44.85 Å / Num. obs: 12567 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 54.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.239 / Rrim(I) all: 0.251 / Net I/σ(I): 8.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.84-3.019.81.11312.0120070.7471.1194100
3.01-3.2211.20.8793.0119000.890.921100
3.22-3.4811.20.6644.1717830.9250.675100
3.48-3.811.10.3896.7916290.9660.408100
3.8-4.2510.90.21311.1514680.9910.224100
4.9-5.989.70.14414.4211300.9940.152100
5.98-8.3911.40.09218.698490.9990.094100
8.39-44.8510.90.05828.115010.9990.05798.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Cootmodel building
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KFQ

6kfq


Resolution: 2.84→44.85 Å / SU ML: 0.3641 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.1236 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2562 2476 9.97 %
Rwork0.2294 22350 -
obs0.2321 12567 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.79 Å2
Refinement stepCycle: LAST / Resolution: 2.84→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 204 17 3691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283775
X-RAY DIFFRACTIONf_angle_d0.57485133
X-RAY DIFFRACTIONf_chiral_restr0.0389598
X-RAY DIFFRACTIONf_plane_restr0.0042599
X-RAY DIFFRACTIONf_dihedral_angle_d12.06422168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.90.32631290.30341220X-RAY DIFFRACTION99.48
2.9-2.950.29341400.27791242X-RAY DIFFRACTION100
2.95-3.020.33071360.28561236X-RAY DIFFRACTION100
3.02-3.090.31721340.2611250X-RAY DIFFRACTION100
3.09-3.170.28431480.26841253X-RAY DIFFRACTION99.86
3.17-3.250.31061440.26861242X-RAY DIFFRACTION99.86
3.25-3.350.27111360.25361232X-RAY DIFFRACTION100
3.35-3.460.3251420.26641278X-RAY DIFFRACTION100
3.46-3.580.30511360.24671223X-RAY DIFFRACTION100
3.58-3.720.2641320.221219X-RAY DIFFRACTION100
3.72-3.890.24981460.21931267X-RAY DIFFRACTION100
3.89-4.10.25021500.20871265X-RAY DIFFRACTION100
4.1-4.350.24861420.22421221X-RAY DIFFRACTION100
4.35-4.690.22271440.20981243X-RAY DIFFRACTION99.93
4.69-5.160.23331220.21971244X-RAY DIFFRACTION100
5.16-5.90.21521390.22581243X-RAY DIFFRACTION99.5
5.9-7.430.21831340.21041247X-RAY DIFFRACTION99.86
7.43-44.850.22941220.18771225X-RAY DIFFRACTION96.21

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