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- PDB-3t45: Crystal structure of bacteriorhodopsin mutant A215T, a phototaxis... -

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Basic information

Entry
Database: PDB / ID: 3t45
TitleCrystal structure of bacteriorhodopsin mutant A215T, a phototaxis signaling mutant at 3.0 A resolution
ComponentsBacteriorhodopsin (GROUND STATE)
KeywordsSIGNALING PROTEIN / Bacteriorhodopsins / Sensory Rhodopsin II / Microbial Rhodopsins / Lipids / Retinaldehyde / Schiff Bases / Light-Sensor / Phototaxis
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / monoatomic ion channel activity / proton transmembrane transport / 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
Chem-LI1 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium sp. NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01 Å
AuthorsOzorowski, G. / Luecke, H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: A transporter converted into a sensor, a phototaxis signaling mutant of bacteriorhodopsin at 3.0 angstrom.
Authors: Spudich, E.N. / Ozorowski, G. / Schow, E.V. / Tobias, D.J. / Spudich, J.L. / Luecke, H.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _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 (GROUND STATE)
B: Bacteriorhodopsin (GROUND STATE)
C: Bacteriorhodopsin (GROUND STATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,08417
Polymers74,2003
Non-polymers7,88414
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-122 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.452, 106.139, 124.845
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: RET / End label comp-ID: RET / Refine code: 1 / Auth seq-ID: 7 - 301 / Label seq-ID: 1

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB - G
21AA - D
12CC - O
22AA - D

NCS ensembles :
ID
1
2
Detailsbiological unit is the same as asym.

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Components

#1: Protein Bacteriorhodopsin (GROUND STATE) / BR / Bacterioopsin / BO


Mass: 24733.291 Da / Num. of mol.: 3 / Mutation: A228T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium sp. NRC-1 (Halophile) / Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-LI1 / 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL / LIPID FRAGMENT


Mass: 639.130 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C42H86O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 3.0M MONOSODIUM PHOSPHATE pH 3.6, vapor diffusion, hanging drop, bicelles, temperature 301K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15545 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.112.90.491192.1
3.11-3.233.10.543194.3
3.23-3.383.30.463197
3.38-3.563.40.363197.9
3.56-3.783.60.257199
3.78-4.073.50.193199.4
4.07-4.483.60.127199.1
4.48-5.133.60.119197.5
5.13-6.463.80.1391100
6.46-503.70.048199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.43 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.01 Å40.37 Å
Translation3.01 Å40.37 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→32.67 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.867 / Occupancy max: 1 / Occupancy min: 1 / SU B: 25.123 / SU ML: 0.449 / Cross valid method: THROUGHOUT / ESU R Free: 0.55 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28752 780 5 %RANDOM
Rwork0.23699 ---
obs0.23958 14757 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.896 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20.02 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.01→32.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5241 0 385 38 5664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025762
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.542.0317800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5985672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91322.069174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03515852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0971521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214005
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 1767 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDRms dev position (Å)
1B3.74
2C3.16
LS refinement shellResolution: 3.007→3.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 56 -
Rwork0.325 962 -
obs--87.99 %

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