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- PDB-4fbz: Crystal structure of deltarhodopsin from Haloterrigena thermotolerans -

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Basic information

Entry
Database: PDB / ID: 4fbz
TitleCrystal structure of deltarhodopsin from Haloterrigena thermotolerans
Componentsdeltarhodopsin
KeywordsMEMBRANE PROTEIN / 7 transmembrane helices / light-driven proton pump / cell membrane
Function / homology
Function and homology information


: / photoreceptor activity / phototransduction / monoatomic ion channel activity / 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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BACTERIORUBERIN / 2,3-DI-PHYTANYL-GLYCEROL / RETINAL / Chem-SQL / Deltarhodopsin
Similarity search - Component
Biological speciesHaloterrigena thermotolerans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKouyama, T.
CitationJournal: Proteins / Year: 2013
Title: Crystal structure of deltarhodopsin-3 from Haloterrigena thermotolerans
Authors: Zhang, J. / Mizuno, K. / Murata, Y. / Koide, H. / Murakami, M. / Ihara, K. / Kouyama, T.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: deltarhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,15810
Polymers26,1681
Non-polymers2,9909
Water21612
1
A: deltarhodopsin
hetero molecules

A: deltarhodopsin
hetero molecules

A: deltarhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,47530
Polymers78,5033
Non-polymers8,97127
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14610 Å2
ΔGint-178 kcal/mol
Surface area27130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.710, 111.710, 198.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein deltarhodopsin


Mass: 26167.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloterrigena thermotolerans (archaea) / Production host: Halobacterium salinarum (Halophile) / Strain (production host): MPK409 / References: UniProt: I4DST7*PLUS
#6: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 19 molecules

#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: Chemical ChemComp-SQL / (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene / squalene / Squalene


Mass: 410.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50
#5: Chemical ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H88O3
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 4.55 Å3/Da / Density % sol: 72.96 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: membrane fusion method, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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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 17, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→86.9 Å / Num. all: 13359 / Num. obs: 13186 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 64.3 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 19.4

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Processing

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

1iw6


Resolution: 2.7→15 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 797 -random
Rwork0.235 ---
obs0.235 13106 98.7 %-
all-13281 --
Displacement parametersBiso mean: 53.1391 Å2
Baniso -1Baniso -2Baniso -3
1--7.481 Å2-16.701 Å20 Å2
2---7.481 Å20 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 154 12 1994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006904
X-RAY DIFFRACTIONc_angle_deg1.17223
X-RAY DIFFRACTIONc_dihedral_angle_d17.86645
X-RAY DIFFRACTIONo_improper_angle_d0.77749

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