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- PDB-3has: Crystal structure of bacteriorhodopsin mutant L152A crystallized ... -

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Basic information

Entry
Database: PDB / ID: 3has
TitleCrystal structure of bacteriorhodopsin mutant L152A crystallized from bicelles
ComponentsBacteriorhodopsin
KeywordsTRANSPORT PROTEIN / bacteriorhodopsin / packing force / van der Waals / evolutionary constraint / membrane protein / integral membrane protein / helical membrane protein / proton transport / Cell membrane / Chromophore / Hydrogen ion transport / Ion transport / Membrane / Photoreceptor protein / Pyrrolidone carboxylic acid / Receptor / Retinal protein / Sensory transduction / Transmembrane / Transport
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / 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
DECANE / DODECANE / HEPTANE / N-OCTANE / HEXADECANE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJoh, N.H. / Yang, D. / Bowie, J.U.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Similar energetic contributions of packing in the core of membrane and water-soluble proteins.
Authors: Joh, N.H. / Oberai, A. / Yang, D. / Whitelegge, J.P. / Bowie, J.U.
History
DepositionMay 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,02311
Polymers26,8871
Non-polymers2,13610
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.169, 102.348, 128.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin / BR


Mass: 26887.420 Da / Num. of mol.: 1 / Mutation: L152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / Strain (production host): L33 / References: UniProt: P02945

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Non-polymers , 8 types, 90 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34
#7: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16
#8: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 310 K / Method: hanging drop, bicelle method / pH: 4
Details: 1.68 M sodium phosphate, 180 mM 1,6-hexanediol, 3.5 % triethylene glycol, PFPC used as cryoprotectant, pH 4.0, hanging drop, bicelle method, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2008
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→90 Å / Num. obs: 23760 / % possible obs: 99.2 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.126 / Χ2: 1.006 / Net I/σ(I): 13.945
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.413 / Num. unique all: 2192 / Χ2: 1.011 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.322 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1893 8 %RANDOM
Rwork0.171 ---
obs0.174 23714 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.36 Å2 / Biso mean: 24.964 Å2 / Biso min: 13.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 134 80 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222059
X-RAY DIFFRACTIONr_angle_refined_deg1.9052.0322813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9715268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72621.87564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14415325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.3341510
X-RAY DIFFRACTIONr_chiral_restr0.1920.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021449
X-RAY DIFFRACTIONr_nbd_refined0.2090.21001
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0250.21
X-RAY DIFFRACTIONr_mcbond_it0.8291.51225
X-RAY DIFFRACTIONr_mcangle_it1.26721932
X-RAY DIFFRACTIONr_scbond_it2.2053981
X-RAY DIFFRACTIONr_scangle_it3.0064.5858
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 126 -
Rwork0.199 1455 -
all-1581 -
obs--91.6 %

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