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- PDB-2ii7: Anabaena sensory rhodopsin transducer -

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Basic information

Entry
Database: PDB / ID: 2ii7
TitleAnabaena sensory rhodopsin transducer
ComponentsAnabaena sensory rhodopsin transducer protein
KeywordsSIGNALING PROTEIN / rhodopsin / transducer
Function / homologyTM1070-like / Anabaena sensory rhodopsin transducer / TM1070-like superfamily / Anabaena sensory rhodopsin transducer / Hypothetical Protein Tm1070; Chain: A / Sandwich / Mainly Beta / Alr3166 protein
Function and homology information
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVogeley, L.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the anabaena sensory rhodopsin transducer.
Authors: Vogeley, L. / Trivedi, V.D. / Sineshchekov, O.A. / Spudich, E.N. / Spudich, J.L. / Luecke, H.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anabaena sensory rhodopsin transducer protein
B: Anabaena sensory rhodopsin transducer protein
C: Anabaena sensory rhodopsin transducer protein
D: Anabaena sensory rhodopsin transducer protein
E: Anabaena sensory rhodopsin transducer protein
F: Anabaena sensory rhodopsin transducer protein
G: Anabaena sensory rhodopsin transducer protein
H: Anabaena sensory rhodopsin transducer protein


Theoretical massNumber of molelcules
Total (without water)117,6358
Polymers117,6358
Non-polymers00
Water27015
1
A: Anabaena sensory rhodopsin transducer protein
B: Anabaena sensory rhodopsin transducer protein
F: Anabaena sensory rhodopsin transducer protein
H: Anabaena sensory rhodopsin transducer protein


Theoretical massNumber of molelcules
Total (without water)58,8174
Polymers58,8174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-50 kcal/mol
Surface area18770 Å2
MethodPISA
2
C: Anabaena sensory rhodopsin transducer protein
D: Anabaena sensory rhodopsin transducer protein
E: Anabaena sensory rhodopsin transducer protein
G: Anabaena sensory rhodopsin transducer protein


Theoretical massNumber of molelcules
Total (without water)58,8174
Polymers58,8174
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-38 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.833, 122.328, 130.131
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Anabaena sensory rhodopsin transducer protein


Mass: 14704.335 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Plasmid: pKJ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8YSC3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM sodium acetate, 10% (w/v) PEG 4000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorDetector: CCD / Date: Feb 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→47.1 Å / Num. obs: 32009 / % possible obs: 86.5 % / Redundancy: 4.41 % / Rmerge(I) obs: 0.103 / Χ2: 0.89 / Net I/σ(I): 7.6 / Scaling rejects: 1427
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.6-2.694.330.5812.31406432500.9589.6
2.69-2.84.360.492.51417432530.8289.2
2.8-2.934.410.3872.91433132500.7988.8
2.93-3.084.430.3093.81431432310.8688.2
3.08-3.284.430.2394.51416731920.8887.7
3.28-3.534.430.1915.81426332091.0387.1
3.53-3.884.430.1317.71432931961.0186.2
3.88-4.454.430.08211.41422731250.9584.6
4.45-5.64.470.05516.11441331270.8283.2
5.6-47.14.410.0419.21437631760.7680.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata processing
CNSrefinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.315 2088 7 %random
Rwork0.259 ---
obs-29668 99.8 %-
Solvent computationBsol: 25.663 Å2
Displacement parametersBiso mean: 61.157 Å2
Baniso -1Baniso -2Baniso -3
1-2.983 Å20 Å20 Å2
2---5.093 Å20 Å2
3---2.109 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 0 15 6555
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_mcbond_it6.3421.5
X-RAY DIFFRACTIONc_scbond_it9.3622
X-RAY DIFFRACTIONc_mcangle_it9.0932
X-RAY DIFFRACTIONc_scangle_it11.7592.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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