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- PDB-2wjl: Bacteriorhodopsin mutant E194D -

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Basic information

Entry
Database: PDB / ID: 2wjl
TitleBacteriorhodopsin mutant E194D
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / ION PUMP / RETINAL PROTEIN / PHOTORECEPTOR PROTEIN / HYDROGEN ION TRANSPORT / PYRROLIDONE / MEROHEDRAL TWINNING / SENSORY TRANSDUCTION / SERPENTINE / CHROMOPHORE / PHOTORECEPTOR
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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPotschies, M. / Wolf, S. / Freier, E. / Hofmann, E. / Gerwert, K.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2010
Title: Directional proton transfer in membrane proteins achieved through protonated protein-bound water molecules: a proton diode.
Authors: Wolf, S. / Freier, E. / Potschies, M. / Hofmann, E. / Gerwert, K.
History
DepositionMay 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 21, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2002
Polymers26,9151
Non-polymers2841
Water30617
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6006
Polymers80,7463
Non-polymers8533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area6410 Å2
ΔGint-52.7 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.220, 61.220, 111.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bacteriorhodopsin / / BR / Bacterioopsin / BO


Mass: 26915.475 Da / Num. of mol.: 1 / Mutation: E194D
Source method: isolated from a genetically manipulated source
Details: RETINAL LINKED VIA SCHIFF BASE TO K216 / Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


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


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 207 TO ASP

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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: 1.84 Å3/Da / Density % sol: 33.1 % / Description: NONE
Crystal growMethod: lipidic cubic phase / pH: 5.6 / Details: LIPID CUBIC PHASE AFTER LUECKE ET AL., pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98407
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98407 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 12843 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.2965 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.18
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 6.16502 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.97 / % possible all: 99.2

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3W

1c3w


Resolution: 2.15→40 Å / Num. parameters: 7072 / Num. restraintsaints: 8545 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
all0.1826 12199 --
obs--94.8 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1756
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 20 17 1756
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0135
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.023
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.078
X-RAY DIFFRACTIONs_approx_iso_adps0

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