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- PDB-3han: Crystal structure of bacteriorhodopsin mutant V49A crystallized f... -

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Basic information

Entry
Database: PDB / ID: 3han
TitleCrystal structure of bacteriorhodopsin mutant V49A 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


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: 2.75 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
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

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1862
Polymers26,9011
Non-polymers2841
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.948, 102.878, 128.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Bacteriorhodopsin / / BR


Mass: 26901.445 Da / Num. of mol.: 1 / Mutation: V49A
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
#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.: 8 / 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: 55.42 %
Crystal growTemperature: 310 K / Method: hanging drop, bicelle method
Details: 1 M sodium phosphate (pH 3.9), 1 M sodium phosphate (pH 4.5), 180 mM 1,6-hexanediol, 3.5% triethyleneglycol, PFPC used as cryoprotectant, hanging drop, bicelle method, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2008
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 7285 / % possible obs: 89.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.105 / Χ2: 1.023 / Net I/σ(I): 10.238
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.382 / Num. unique all: 421 / Χ2: 0.932 / % possible all: 52.8

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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: 2.75→41.2 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.038 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 588 8.1 %RANDOM
Rwork0.222 ---
obs0.227 7263 89.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.96 Å2 / Biso mean: 40.424 Å2 / Biso min: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.75→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 20 8 1771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0221813
X-RAY DIFFRACTIONr_angle_refined_deg2.861.9842475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18222.06958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53315282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.348157
X-RAY DIFFRACTIONr_chiral_restr0.2460.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021330
X-RAY DIFFRACTIONr_nbd_refined0.2510.2854
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21246
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.221
X-RAY DIFFRACTIONr_mcbond_it1.4131.51176
X-RAY DIFFRACTIONr_mcangle_it2.25521787
X-RAY DIFFRACTIONr_scbond_it3.5793821
X-RAY DIFFRACTIONr_scangle_it5.2844.5688
LS refinement shellResolution: 2.75→2.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 23 -
Rwork0.225 246 -
all-269 -
obs--45.06 %

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