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- PDB-5ahy: Halorhodopsin from Halobacterium salinarum in a new rhombohedral ... -

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Basic information

Entry
Database: PDB / ID: 5ahy
TitleHalorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form
ComponentsHALORHODOPSIN
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / HALOPHILIC ARCHAEA / ARCHAEAL RHODOPSIN / LIGHT DRIVEN ION PUMP / RETINAL PROTEIN / ION TRANSMEMBRANE TRANSPORT
Function / homology
Function and homology information


photoreceptor activity / phototransduction / 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
RETINAL / Halorhodopsin
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSchreiner, M. / Schlesinger, R. / Heberle, J. / Niemann, H.H.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structure of Halorhodopsin from Halobacterium Salinarum in a New Crystal Form that Imposes Little Restraint on the E-F Loop.
Authors: Schreiner, M. / Schlesinger, R. / Heberle, J. / Niemann, H.H.
History
DepositionFeb 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Jan 10, 2024Group: 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: HALORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5935
Polymers27,9461
Non-polymers6484
Water50428
1
A: HALORHODOPSIN
hetero molecules

A: HALORHODOPSIN
hetero molecules

A: HALORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,78015
Polymers83,8373
Non-polymers1,94312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area8250 Å2
ΔGint-149.1 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.651, 103.651, 138.588
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein HALORHODOPSIN /


Mass: 27945.709 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-274
Source method: isolated from a genetically manipulated source
Details: IMINE BOND (SCHIFF BASE) BETWEEN NZ OF LYS242 AND C15 OF THE RETINAL LIGAND
Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: L33 / Production host: HALOBACTERIUM SALINARUM (Halophile) / Strain (production host): L33 / References: UniProt: B0R2U4
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRETINAL (RET): C15 COVALENTLY LINKED TO LYS242 NZ VIA SCHIFF BASE
Sequence detailsAMINO ACIDS 1-19 ARE MISSING (CLEAVED SIGNAL PEPTIDE), C- TERMINAL HEXAHISTIDIN-TAG

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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: 2.78 Å3/Da / Density % sol: 55.74 % / Description: NONE
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: RESERVOIR SOLUTION: 100 MM CITRATE PH 8, 150 MM NACL, 2.1-2.4 M (NH4)2SO4. VAPOR DIFFUSION AT 296 K WITH DROP RATIO OF 1.2 TO 0.8 UL PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 6 MG/ML.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2012 / Details: PT COATED SI MIRROR
RadiationMonochromator: CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.15→42.7 Å / Num. obs: 15809 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 29.72 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.9
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E12

1e12


Resolution: 2.15→42.699 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 796 5 %
Rwork0.1851 --
obs0.1873 15804 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.4 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 42 28 1892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081942
X-RAY DIFFRACTIONf_angle_d1.0712667
X-RAY DIFFRACTIONf_dihedral_angle_d12.599656
X-RAY DIFFRACTIONf_chiral_restr0.041332
X-RAY DIFFRACTIONf_plane_restr0.005318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.28470.26191470.21142449X-RAY DIFFRACTION100
2.2847-2.46110.27441300.19142477X-RAY DIFFRACTION100
2.4611-2.70870.25171190.17982493X-RAY DIFFRACTION100
2.7087-3.10060.23651380.16672471X-RAY DIFFRACTION100
3.1006-3.9060.19251260.17882524X-RAY DIFFRACTION100
3.906-42.70730.2181360.19162594X-RAY DIFFRACTION100

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