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- PDB-1tn5: Structure of bacterorhodopsin mutant K41P -

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Basic information

Entry
Database: PDB / ID: 1tn5
TitleStructure of bacterorhodopsin mutant K41P
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / bacteriorhodopsin / bicelle
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: 2.2 Å
AuthorsYohannan, S. / Yang, D. / Faham, S. / Boulting, G. / Whitelegge, J. / Bowie, J.U.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Proline substitutions are not easily accommodated in a membrane protein
Authors: Yohannan, S. / Yang, D. / Faham, S. / Boulting, G. / Whitelegge, J. / Bowie, J.U.
History
DepositionJun 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 27, 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
Remark 600HETEROGEN ATOM O1 OF RETINAL MISSING DUE TO COVALENT BOND WITH RESIDUE 216 OF BACTERIORHODOPSIN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3644
Polymers53,7952
Non-polymers5692
Water61334
1
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1822
Polymers26,8971
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1822
Polymers26,8971
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.36, 109.12, 55.77
Angle α, β, γ (deg.)90.00, 113.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacteriorhodopsin / / BR


Mass: 26897.434 Da / Num. of mol.: 2 / Mutation: K41P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Strain: L33 / Gene: BOP, VNG1467G / Production host: Escherichia coli (E. coli) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 4
Details: sodium phosphate, hexanediol, DMPC/CHAPSO, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 25820 / Num. obs: 25820 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 88.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Crystal twinning was observed. Twinning operation = -h,-k,h+l. Twinning fraction = 0.5
RfactorNum. reflectionSelection details
Rfree0.299 1153 SHELLS
Rwork0.249 --
all0.252 21063 -
obs0.252 19910 -
Solvent computationBsol: 93.1784 Å2 / ksol: 0.408664 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.473 Å20 Å21.757 Å2
2---20.884 Å20 Å2
3---10.411 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 40 34 3582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_angle_d0.99
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3ret.par

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