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- PDB-4kly: Crystal structure of a blue-light absorbing proteorhodopsin mutan... -

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Basic information

Entry
Database: PDB / ID: 4kly
TitleCrystal structure of a blue-light absorbing proteorhodopsin mutant D97N from HOT75
ComponentsBlue-light absorbing proteorhodopsin
KeywordsPROTON TRANSPORT / Ion transport / proton pump / Retinylidene Schiff base / Membrane
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / plasma membrane
Similarity search - Function
Proteorhodopsin / 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 / Blue-light absorbing proteorhodopsin
Similarity search - Component
Biological speciesgamma proteobacterium 'Hot 75m4' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsRan, T. / Ozorowski, G. / Gao, Y. / Wang, W. / Luecke, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes.
Authors: Ran, T. / Ozorowski, G. / Gao, Y. / Sineshchekov, O.A. / Wang, W. / Spudich, J.L. / Luecke, H.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Other
Revision 1.2Oct 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blue-light absorbing proteorhodopsin
B: Blue-light absorbing proteorhodopsin
C: Blue-light absorbing proteorhodopsin
D: Blue-light absorbing proteorhodopsin
E: Blue-light absorbing proteorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,38910
Polymers141,9675
Non-polymers1,4225
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-85 kcal/mol
Surface area45080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.100, 168.800, 65.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Blue-light absorbing proteorhodopsin / BPR


Mass: 28393.406 Da / Num. of mol.: 5 / Mutation: D97N / Source method: isolated from a natural source
Source: (natural) gamma proteobacterium 'Hot 75m4' (bacteria)
References: UniProt: Q9AFF7
#2: Chemical
ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 mg/mL protein plus 1-2% Tween 80 in a 1:1 ratio with reservoir solution (0.2 M ammonium acetate, 0.1 M bis-tris pH 6.5, 44-49% [w/v] MPD), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorDate: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.72→20 Å / Num. obs: 48838 / % possible obs: 99.6 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.227 / Net I/σ(I): 8.07
Reflection shellResolution: 2.72→2.97 Å / Redundancy: 11.18 % / Rmerge(I) obs: 3.116 / Mean I/σ(I) obs: 1.03 / Num. unique all: 11202 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHELXSphasing
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.636 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26081 2547 5.1 %RANDOM
Rwork0.20922 ---
obs0.21181 47520 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8724 0 100 13 8837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.029062
X-RAY DIFFRACTIONr_bond_other_d0.0020.028732
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.97312364
X-RAY DIFFRACTIONr_angle_other_deg0.848319906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76251123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2723.47317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.396151199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.931515
X-RAY DIFFRACTIONr_chiral_restr0.1940.21419
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022161
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 209 -
Rwork0.333 3359 -
obs--98.97 %

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