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- PDB-5kkh: 2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Ha... -

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Basic information

Entry
Database: PDB / ID: 5kkh
Title2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Haloquadratum walsbyi (HwBR) at 100 K
ComponentsBacteriorhodopsin-I
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


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
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin-I
Similarity search - Component
Biological speciesHaloquadratum walsbyi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.125 Å
AuthorsBroecker, J. / Ernst, O.P.
Funding support Canada, Germany, 2items
OrganizationGrant numberCountry
Government of CanadaCanada Excellence Research Chair Canada
German Research Foundation (DFG)BR 5124/1-1 Germany
CitationJournal: Cryst Growth Des / Year: 2016
Title: A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals.
Authors: Broecker, J. / Klingel, V. / Ou, W.L. / Balo, A.R. / Kissick, D.J. / Ogata, C.M. / Kuo, A. / Ernst, O.P.
History
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin-I
B: Bacteriorhodopsin-I
C: Bacteriorhodopsin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,41315
Polymers87,3503
Non-polymers4,06212
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-49 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.110, 61.270, 119.030
Angle α, β, γ (deg.)90.00, 116.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriorhodopsin-I / HwBR / Squarebop I


Mass: 29116.809 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloquadratum walsbyi (strain DSM 16790 / HBSQ001) (archaea)
Strain: DSM 16790 / HBSQ001 / Gene: bop1, bopI, HQ_1014A / Production host: Escherichia coli (E. coli) / References: UniProt: Q18DH8
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.7 % / Description: small compact, hexagonal plates
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: 8% (v/v) Tacsimate, 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.125→29.45 Å / Num. all: 57569 / Num. obs: 35323 / % possible obs: 91 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.86 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.26
Reflection shellResolution: 2.13→2.2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.66 / % possible all: 70

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EI4

2ei4


Resolution: 2.125→29.446 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1755 4.98 %
Rwork0.2129 --
obs0.2138 57569 90.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.125→29.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5277 0 285 84 5646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095728
X-RAY DIFFRACTIONf_angle_d1.7747765
X-RAY DIFFRACTIONf_dihedral_angle_d18.6932079
X-RAY DIFFRACTIONf_chiral_restr0.049920
X-RAY DIFFRACTIONf_plane_restr0.005932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1246-2.1820.18211120.20321894X-RAY DIFFRACTION68
2.182-2.24620.20961140.20042013X-RAY DIFFRACTION72
2.2462-2.31870.22031400.20722238X-RAY DIFFRACTION80
2.3187-2.40150.18461110.19722561X-RAY DIFFRACTION91
2.4015-2.49760.19961310.20152596X-RAY DIFFRACTION92
2.4976-2.61120.21971590.20032565X-RAY DIFFRACTION92
2.6112-2.74880.19451240.20652708X-RAY DIFFRACTION95
2.7488-2.92090.20491520.20162719X-RAY DIFFRACTION95
2.9209-3.14620.25771550.21392670X-RAY DIFFRACTION96
3.1462-3.46240.2541540.20822836X-RAY DIFFRACTION100
3.4624-3.96230.26011480.21662858X-RAY DIFFRACTION100
3.9623-4.98820.22881180.21472888X-RAY DIFFRACTION100
4.9882-29.44920.29751370.25012956X-RAY DIFFRACTION100

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