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- PDB-2jag: L1-intermediate of halorhodopsin T203V -

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Basic information

Entry
Database: PDB / ID: 2jag
TitleL1-intermediate of halorhodopsin T203V
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / CHROMOPHORE / CHLORIDE PUMP / ION TRANSPORT / SENSORY TRANSDUCTION / MEMBRANE / CHLORIDE / RECEPTOR / ION PUMP / TRANSPORT / PHOTORECEPTOR PROTEIN / TRANSMEMBRANE / RETINAL PROTEIN / INTERMEDIATE L1
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
PALMITIC ACID / RETINAL / Halorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsGmelin, W. / Zeth, K. / Efremov, R. / Heberle, J. / Tittor, J. / Oesterhelt, D.
CitationJournal: Photochem. Photobiol. / Year: 2007
Title: The crystal structure of the L1 intermediate of halorhodopsin at 1.9 angstroms resolution.
Authors: Gmelin, W. / Zeth, K. / Efremov, R. / Heberle, J. / Tittor, J. / Oesterhelt, D.
History
DepositionNov 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description
Revision 1.2Nov 21, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Jul 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 1.4Dec 13, 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

Downloads & links

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Assembly

Deposited unit
A: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7616
Polymers28,8571
Non-polymers9045
Water73941
1
A: Halorhodopsin
hetero molecules

A: Halorhodopsin
hetero molecules

A: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,28318
Polymers86,5703
Non-polymers2,71215
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 area11690 Å2
ΔGint-159.5 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.042, 95.042, 157.674
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, 2 molecules A

#1: Protein Halorhodopsin / / HR


Mass: 28856.814 Da / Num. of mol.: 1 / Mutation: T203V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1) (Halophile)
Description: DSM 671 / Gene: hop, OE_1299R / Production host: Halobacterium salinarum (Halophile) / References: UniProt: B0R2U4
#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

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Non-polymers , 4 types, 45 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 203 TO VAL ENGINEERED RESIDUE IN CHAIN A, VAL 229 TO ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.2 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 23209 / % possible obs: 87.8 % / Observed criterion σ(I): 3.5 / Redundancy: 8.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.1
Reflection shellRedundancy: 8.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.2 / % possible all: 73.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E12

1e12


Resolution: 1.93→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 3-10 HELIX DISTORTION BETWEEN LEU A 110 AND ALA A 113. PI-BULGE BETWEEN ALA A 178 AND TRP A 183 DISRUPTS HELIX E.RETINAL IN 13-CIS CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 959 4.6 %RANDOM
Rwork0.2373 ---
obs0.2373 19178 91.9 %-
Solvent computationBsol: 99.7591 Å2 / ksol: 0.488806 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.859 Å20.219 Å20 Å2
2--0.859 Å20 Å2
3----1.718 Å2
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 60 41 1923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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