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- PDB-8r96: Crystal structure of the cryorhodopsin CryoR2 at pH 4.6, type A c... -

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Basic information

Entry
Database: PDB / ID: 8r96
TitleCrystal structure of the cryorhodopsin CryoR2 at pH 4.6, type A crystals
Componentscryorhodopsin
KeywordsMEMBRANE PROTEIN / retinal / rhodopsin / photocycle
Function / homologyEICOSANE / OLEIC ACID / PHOSPHATE ION / RETINAL
Function and homology information
Biological speciesSubtercola endophyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsKovalev, K. / Lamm, G.H.U. / Marin, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND847543 Germany
CitationJournal: To Be Published
Title: CryoRhodopsins: a new clade of microbial rhodopsins from cold environments
Authors: Lamm, G.H.U. / Marin, E. / Guskov, A. / Kovalev, K.
History
DepositionNov 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cryorhodopsin
B: cryorhodopsin
C: cryorhodopsin
D: cryorhodopsin
E: cryorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,00330
Polymers174,8685
Non-polymers6,13525
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25230 Å2
ΔGint-77 kcal/mol
Surface area47520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.565, 295.665, 185.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
cryorhodopsin


Mass: 34973.539 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Subtercola endophyticus (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 56 molecules

#2: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C20H28O / Source: (gene. exp.) Subtercola endophyticus (bacteria) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.6 / Details: 1.2M Na/K-Pi pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.457→92.75 Å / Num. obs: 56393 / % possible obs: 65.6 % / Redundancy: 13.44 % / CC1/2: 0.9964 / Rpim(I) all: 0.064 / Net I/σ(I): 8.493
Reflection shellResolution: 2.457→2.719 Å / Num. unique obs: 38364 / CC1/2: 0.304 / Rpim(I) all: 0.962

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
STARANISOdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.926 / SU B: 16.383 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25445 2746 4.9 %RANDOM
Rwork0.23874 ---
obs0.23952 53453 65.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.574 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å20 Å2
2---1.1 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 2.46→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10838 0 175 31 11044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311238
X-RAY DIFFRACTIONr_bond_other_d00.01511134
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.62615377
X-RAY DIFFRACTIONr_angle_other_deg1.0671.55525355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.53451435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.4620.392434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.734151565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6421545
X-RAY DIFFRACTIONr_chiral_restr0.0260.21580
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212480
X-RAY DIFFRACTIONr_gen_planes_other00.022530
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.726.1465755
X-RAY DIFFRACTIONr_mcbond_other4.7196.1465754
X-RAY DIFFRACTIONr_mcangle_it7.4089.2217185
X-RAY DIFFRACTIONr_mcangle_other7.4089.2217186
X-RAY DIFFRACTIONr_scbond_it4.7346.4215483
X-RAY DIFFRACTIONr_scbond_other4.7586.4215484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3249.5138193
X-RAY DIFFRACTIONr_long_range_B_refined10.23875.31912944
X-RAY DIFFRACTIONr_long_range_B_other10.23875.3212945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A93580.05
12B93580.05
21A93420.05
22C93420.05
31A93120.06
32D93120.06
41A93370.06
42E93370.06
51B93320.05
52C93320.05
61B93100.06
62D93100.06
71B93060.06
72E93060.06
81C93140.06
82D93140.06
91C93250.06
92E93250.06
101D93150.05
102E93150.05
LS refinement shellResolution: 2.46→2.52 Å
RfactorNum. reflection% reflection
Rfree0.334 9 -
Rwork0.427 208 -
obs--3.49 %

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