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- PDB-8r98: Crystal structure of the cryorhodopsin CryoR2 at pH 4.6, type B c... -

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Basic information

Entry
Database: PDB / ID: 8r98
TitleCrystal structure of the cryorhodopsin CryoR2 at pH 4.6, type B crystals, illuminated state
Componentscryorhodopsin CryoR2
KeywordsMEMBRANE PROTEIN / retinal / rhodopsin / photocycle
Function / homologyEICOSANE / OLEIC ACID / PHOSPHATE ION / RETINAL
Function and homology information
Biological speciesSubtercola sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 CryoR2
B: cryorhodopsin CryoR2
C: cryorhodopsin CryoR2
D: cryorhodopsin CryoR2
E: cryorhodopsin CryoR2
H: cryorhodopsin CryoR2
G: cryorhodopsin CryoR2
F: cryorhodopsin CryoR2
I: cryorhodopsin CryoR2
K: cryorhodopsin CryoR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,00660
Polymers349,73510
Non-polymers12,27050
Water00
1
A: cryorhodopsin CryoR2
B: cryorhodopsin CryoR2
C: cryorhodopsin CryoR2
D: cryorhodopsin CryoR2
E: cryorhodopsin CryoR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,00330
Polymers174,8685
Non-polymers6,13525
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24630 Å2
ΔGint-84 kcal/mol
Surface area47690 Å2
MethodPISA
2
H: cryorhodopsin CryoR2
G: cryorhodopsin CryoR2
F: cryorhodopsin CryoR2
I: cryorhodopsin CryoR2
K: cryorhodopsin CryoR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,00330
Polymers174,8685
Non-polymers6,13525
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24800 Å2
ΔGint-86 kcal/mol
Surface area47670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.108, 84.964, 296.943
Angle α, β, γ (deg.)90.00, 96.87, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515
1616
1717
1818
1919
2020
2121
2222
2323
2424
2525
2626
2727
2828
2929
3030
3131
3232
3333
3434
3535
3636
3737
3838
3939
4040
4141
4242
4343
4444
4545

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

#1: Protein
cryorhodopsin CryoR2


Mass: 34973.539 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Subtercola sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C20H28O / Source: (gene. exp.) Subtercola sp. (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.: 2 / Source method: obtained synthetically / Formula: C18H34O2
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: 2.67 Å3/Da / Density % sol: 53.89 %
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: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.774→74.387 Å / Num. obs: 59820 / % possible obs: 63.34 % / Redundancy: 6.88 % / CC1/2: 0.9987 / Rpim(I) all: 0.085 / Net I/σ(I): 6.512
Reflection shellResolution: 2.774→3.1 Å / Num. unique obs: 4018 / CC1/2: 0.3825 / Rpim(I) all: 1.061

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / SU B: 43.242 / SU ML: 0.663 / Cross valid method: THROUGHOUT / ESU R Free: 0.649 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30938 2850 4.9 %RANDOM
Rwork0.28701 ---
obs0.28814 54950 77.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å2-0 Å2-0.08 Å2
2--0.95 Å2-0 Å2
3----2.74 Å2
Refinement stepCycle: 1 / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21522 0 326 0 21848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01322293
X-RAY DIFFRACTIONr_bond_other_d0.0040.01522024
X-RAY DIFFRACTIONr_angle_refined_deg1.071.62530520
X-RAY DIFFRACTIONr_angle_other_deg1.1371.55550122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.65852861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.3520.426846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.979153077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.4891585
X-RAY DIFFRACTIONr_chiral_restr0.0320.23151
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0224800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025010
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_it5.4859.1711477
X-RAY DIFFRACTIONr_mcbond_other5.4849.1711476
X-RAY DIFFRACTIONr_mcangle_it8.87113.75814327
X-RAY DIFFRACTIONr_mcangle_other8.87113.75814328
X-RAY DIFFRACTIONr_scbond_it5.4359.4510816
X-RAY DIFFRACTIONr_scbond_other5.4279.43410777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.94114.05916134
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)
11A91810.08
12B91810.08
21A91400.08
22C91400.08
31A91990.07
32D91990.07
41A91320.07
42E91320.07
51A91340.08
52H91340.08
61A92880.06
62G92880.06
71A92150.08
72F92150.08
81A91750.06
82I91750.06
91A91420.07
92K91420.07
101B92340.08
102C92340.08
111B93450.07
112D93450.07
121B92740.08
122E92740.08
131B92020.08
132H92020.08
141B93960.07
142G93960.07
151B94910.06
152F94910.06
161B93730.07
162I93730.07
171B93040.07
172K93040.07
181C92120.08
182D92120.08
191C91370.08
192E91370.08
201C93260.06
202H93260.06
211C92420.08
212G92420.08
221C92300.08
222F92300.08
231C92270.08
232I92270.08
241C91750.08
242K91750.08
251D92510.07
252E92510.07
261D92090.08
262H92090.08
271D93480.07
272G93480.07
281D93290.07
282F93290.07
291D93950.05
292I93950.05
301D92720.07
302K92720.07
311E91350.08
312H91350.08
321E92580.07
322G92580.07
331E92710.08
332F92710.08
341E92700.06
342I92700.06
351E93460.05
352K93460.05
361H92100.08
362G92100.08
371H91790.08
372F91790.08
381H92000.08
382I92000.08
391H91500.08
392K91500.08
401G93330.08
402F93330.08
411G93340.07
412I93340.07
421G92750.07
422K92750.07
431F93300.07
432I93300.07
441F92770.08
442K92770.08
451I92870.06
452K92870.06
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.493 91 -
Rwork0.495 1572 -
obs--30.91 %

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