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- PDB-3cod: Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 3cod
TitleCrystal Structure of T90A/D115A mutant of Bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / membrane protein / membrane protein folding / hydrogen bond / Chromophore / Hydrogen ion transport / Ion transport / 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 / Resolution: 2.7 Å
AuthorsJoh, N.H. / Min, A. / Faham, S. / Bowie, J.U.
CitationJournal: Nature / Year: 2008
Title: Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins.
Authors: Joh, N.H. / Min, A. / Faham, S. / Whitelegge, J.P. / Yang, D. / Woods, V.L. / Bowie, J.U.
History
DepositionMar 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2804
Polymers53,7112
Non-polymers5692
Water68538
1
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1402
Polymers26,8551
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1402
Polymers26,8551
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.974, 109.658, 55.517
Angle α, β, γ (deg.)90.000, 113.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacteriorhodopsin / / BR


Mass: 26855.463 Da / Num. of mol.: 2 / Mutation: T103A, D128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop / 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.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 310 K / pH: 3.7
Details: 2.4 M NaH2PO4 (pH 3.7), 3.5% triethylene glycerol, and 0.15 M hexanediol, 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: Sep 16, 2006
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: -h,-k,h+l / Fraction: 0.5
ReflectionResolution: 2.7→40 Å / Num. obs: 12143 / % possible obs: 91 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.134 / Χ2: 0.993 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.82.10.2198750.98365.1
2.8-2.912.40.27910090.99776.2
2.91-3.042.60.24211370.99687.5
3.04-3.22.70.22312481.00892.7
3.2-3.42.80.19412880.97396.8
3.4-3.662.90.16512850.95796.9
3.66-4.032.80.14313140.97798.6
4.03-4.6230.11813161.02398.1
4.62-5.813.10.11613071.00299.1
5.81-403.20.0713641.00299.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
BOSdata collection
CNSphasing
RefinementResolution: 2.7→40 Å / σ(F): 533
RfactorNum. reflection% reflection
Rfree0.287 605 4.5 %
Rwork0.273 --
obs-11592 87 %
Solvent computationBsol: 78.937 Å2
Displacement parametersBiso mean: 33.335 Å2
Baniso -1Baniso -2Baniso -3
1--1.086 Å20 Å20.812 Å2
2--18.611 Å20 Å2
3----17.525 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 40 38 3580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond length0.005
X-RAY DIFFRACTIONbond angle1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3top

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