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- PDB-1e0p: L intermediate of bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 1e0p
TitleL intermediate of bacteriorhodopsin
ComponentsBACTERIORHODOPSIN, GROUND STATE
KeywordsTRANSPORT / ION TRANSPORT / PHOTORECEPTOR / TRANSMEMBRANE / RETINAL PROTEIN HYDROGEN ION 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 SALINARIUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsRoyant, A. / Edman, K. / Ursby, T. / Pebay-Peyroula, E. / Landau, E.M. / Neutze, R.
CitationJournal: Nature / Year: 2000
Title: Helix Deformation is Coupled to Vectorial Proton Transport in Bacteriorhodopsin'S Photocycle
Authors: Royant, A. / Edman, K. / Ursby, T. / Pebay-Peyroula, E. / Landau, E.M. / Neutze, R.
History
DepositionApr 4, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERIORHODOPSIN, GROUND STATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2752
Polymers24,9911
Non-polymers2841
Water54030
1
A: BACTERIORHODOPSIN, GROUND STATE
hetero molecules

A: BACTERIORHODOPSIN, GROUND STATE
hetero molecules

A: BACTERIORHODOPSIN, GROUND STATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8256
Polymers74,9723
Non-polymers8533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area6230 Å2
ΔGint-50.93 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.960, 60.960, 109.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein BACTERIORHODOPSIN, GROUND STATE /


Mass: 24990.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CONFORMER B IS GROUND STATE, CONFORMER A IS THE L-STATE FORM.
Source: (natural) HALOBACTERIUM SALINARIUM (Halophile) / Strain: S9 / 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.: 30 / Source method: isolated from a natural source / Formula: H2O
Compound detailsALTERNATE CONFORMER B GROUND STATE MODEL FROM 1QHJ ALTERNATE CONFORMER A L-STATE MODEL

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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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growpH: 5.6
Details: PROTEIN FROM THE PURPLE MEMBRANE WAS RESOLVED IN OCTYL GLUC, pH 5.60
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.3 Msodium potassium Pi11
23.5 mg/mlprotein11
30.05 %methylpentandiol11
41.2 %beta-octylglycopyranoside11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→30.5 Å / Num. obs: 13088 / % possible obs: 96.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.063 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.521 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 73411 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.521

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.1→30.5 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2443186 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE COORDINATE FILE CONTAINS 2 MODELS CHAINS A AND B, ONLY A WAS REFINED, B WAS FIXED DURING THE WHOLE REFINEMENT. THE NUMBER OF ATOMS USED IN THE REFINEMENT REFERES TO CHAIN A. FREE R VALUE ...Details: THE COORDINATE FILE CONTAINS 2 MODELS CHAINS A AND B, ONLY A WAS REFINED, B WAS FIXED DURING THE WHOLE REFINEMENT. THE NUMBER OF ATOMS USED IN THE REFINEMENT REFERES TO CHAIN A. FREE R VALUE TEST SET SAME AS PREVIOUS REFINEMENTS 1QHJ, 1QKP, 1QKO
RfactorNum. reflection% reflectionSelection details
Rfree0.288 593 4.6 %RANDOM
Rwork0.265 ---
obs0.265 12912 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.56 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å2-0.4 Å20 Å2
2---3.96 Å20 Å2
3---7.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 20 30 1802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 87 4 %
Rwork0.289 2111 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3RETFIN-CIS.PARRETFIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor obs: 0.2935

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