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- PDB-4jr8: Crystal structure of cruxrhodopsin-3 from Haloarcula vallismortis... -

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Basic information

Entry
Database: PDB / ID: 4jr8
TitleCrystal structure of cruxrhodopsin-3 from Haloarcula vallismortis at 2.3 angstrom resolution
ComponentsCruxrhodopsin-3
KeywordsPROTON TRANSPORT / protein-bacteioruberin complex / seven transmembrane alpha helices / light-driven proton pump / Membrane
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane
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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BACTERIORUBERIN / RETINAL / Cruxrhodopsin-3
Similarity search - Component
Biological speciesHaloarcula vallismortis (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKouyama, T. / Chan, S.K.
CitationJournal: Plos One / Year: 2014
Title: Crystal structure of Cruxrhodopsin-3 from Haloarcula vallismortis
Authors: Chan, S.K. / Kitajima-Ihara, T. / Fujii, R. / Gotoh, T. / Murakami, M. / Ihara, K. / Kouyama, T.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cruxrhodopsin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8933
Polymers26,8671
Non-polymers1,0262
Water25214
1
A: Cruxrhodopsin-3
hetero molecules

A: Cruxrhodopsin-3
hetero molecules

A: Cruxrhodopsin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6789
Polymers80,6023
Non-polymers3,0776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10570 Å2
ΔGint-54 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.21, 106.21, 60.21
Angle α, β, γ (deg.)90, 90, 120
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Cruxrhodopsin-3 / COP-3 / CR-3


Mass: 26867.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula vallismortis (Halophile) / Gene: cop3 / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P94854
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-22B / BACTERIORUBERIN / Halobacterium


Mass: 741.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H76O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.1M ammonium sulfate, 0.1M sodium citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2012
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.9 Å / Num. all: 17545 / Num. obs: 15610 / % possible obs: 90 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 5.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 21.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2299 / Rsym value: 0.448 / % possible all: 92.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1iw6

1iw6


Resolution: 2.3→15 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.295 763 RANDOM
Rwork0.245 --
all0.254 15873 -
obs0.254 14285 -
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.085 Å21.862 Å20 Å2
2--5.085 Å20 Å2
3----10.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.16 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 57 14 1872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.79

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