[English] 日本語
Yorodumi
- PDB-8r97: Crystal structure of the cryorhodopsin CryoR2 at pH 4.6, type B c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r97
TitleCrystal structure of the cryorhodopsin CryoR2 at pH 4.6, type B crystals, non-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 area25450 Å2
ΔGint-79 kcal/mol
Surface area46610 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 area25470 Å2
ΔGint-85 kcal/mol
Surface area46710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.763, 84.984, 296.404
Angle α, β, γ (deg.)90.00, 96.83, 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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.6 / Details: 1.2M Na/K-Pi pH 4.6

-
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: 2.718→74.351 Å / Num. obs: 67679 / % possible obs: 67.67 % / Redundancy: 6.57 % / CC1/2: 0.9984 / Rpim(I) all: 0.085 / Net I/σ(I): 6.126
Reflection shellResolution: 2.718→3.046 Å / Num. unique obs: 4230 / CC1/2: 0.4325 / Rpim(I) all: 1.049

-
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: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 36.909 / SU ML: 0.583 / Cross valid method: THROUGHOUT / ESU R Free: 0.576 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30083 3192 4.9 %RANDOM
Rwork0.26576 ---
obs0.26752 61380 86.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å2-0.23 Å2
2--1 Å20 Å2
3----1.72 Å2
Refinement stepCycle: 1 / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21608 0 345 0 21953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01322399
X-RAY DIFFRACTIONr_bond_other_d00.01522192
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.62530653
X-RAY DIFFRACTIONr_angle_other_deg1.0771.55550526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.64152864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.72520.36861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.488153121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8091590
X-RAY DIFFRACTIONr_chiral_restr0.0310.23154
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0224876
X-RAY DIFFRACTIONr_gen_planes_other00.025040
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_it8.038.80111486
X-RAY DIFFRACTIONr_mcbond_other8.038.80111485
X-RAY DIFFRACTIONr_mcangle_it12.24713.20714340
X-RAY DIFFRACTIONr_mcangle_other12.24713.20714341
X-RAY DIFFRACTIONr_scbond_it8.0339.19210913
X-RAY DIFFRACTIONr_scbond_other8.0149.17910874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.22113.60316254
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)
11A94060.06
12B94060.06
21A93350.06
22C93350.06
31A93460.07
32D93460.07
41A93270.06
42E93270.06
51A92760.07
52H92760.07
61A95040.04
62G95040.04
71A94090.06
72F94090.06
81A92810.06
82I92810.06
91A93360.06
92K93360.06
101B92860.07
102C92860.07
111B93700.07
112D93700.07
121B93520.07
122E93520.07
131B92580.07
132H92580.07
141B94090.06
142G94090.06
151B96100.03
152F96100.03
161B93440.07
162I93440.07
171B93560.07
172K93560.07
181C92720.07
182D92720.07
191C92360.07
192E92360.07
201C94390.04
202H94390.04
211C92760.07
212G92760.07
221C93080.07
222F93080.07
231C92100.07
232I92100.07
241C92310.07
242K92310.07
251D92980.06
252E92980.06
261D92470.07
262H92470.07
271D93680.07
272G93680.07
281D93780.07
282F93780.07
291D94030.05
292I94030.05
301D93050.06
302K93050.06
311E91880.07
312H91880.07
321E93080.06
322G93080.06
331E93550.06
332F93550.06
341E92970.06
342I92970.06
351E95260.03
352K95260.03
361H92460.07
362G92460.07
371H92660.07
372F92660.07
381H92040.07
382I92040.07
391H91760.07
392K91760.07
401G94070.06
402F94070.06
411G92940.06
412I92940.06
421G92990.07
422K92990.07
431F93270.06
432I93270.06
441F93450.07
442K93450.07
451I92960.06
452K92960.06
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.543 136 -
Rwork0.489 2321 -
obs--45.58 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more