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- PDB-2iia: Anabaena sensory rhodopsin transducer -

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Basic information

Entry
Database: PDB / ID: 2iia
TitleAnabaena sensory rhodopsin transducer
ComponentsSensory 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 / SAD / Resolution: 1.8 Å
AuthorsVogeley, L. / Sineshchekov, O.A. / Trivedi, V.D. / Spudich, E.N. / Spudich, J.L. / Luecke, H.
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: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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

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Assembly

Deposited unit
A: Sensory rhodopsin transducer protein


Theoretical massNumber of molelcules
Total (without water)14,7041
Polymers14,7041
Non-polymers00
Water2,162120
1
A: Sensory rhodopsin transducer protein

A: Sensory rhodopsin transducer protein

A: Sensory rhodopsin transducer protein

A: 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
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area4740 Å2
ΔGint-32 kcal/mol
Surface area16570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.274, 57.274, 39.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
DetailsThe biological unit is a tetramer generated from the monomer in the asymmetric unit by the operations:

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Components

#1: Protein Sensory rhodopsin transducer protein


Mass: 14704.339 Da / Num. of mol.: 1
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 / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM sodium acetate, pH 4.6 and 7 to 11% (w/v) polyethylene glycol (PEG) 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2
DetectorDetector: CCD / Date: Sep 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 11936 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.031 / Χ2: 0.573 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.833.50.2145370.401192
1.83-1.863.90.175910.413199
1.86-1.94.40.1425990.444199.7
1.9-1.944.50.1356090.481199.8
1.94-1.984.50.1075970.4621100
1.98-2.034.60.0986020.4731100
2.03-2.084.50.0895880.5361100
2.08-2.134.60.0746180.541100
2.13-2.24.60.0656040.5071100
2.2-2.274.60.065920.5261100
2.27-2.354.70.0546020.562199.7
2.35-2.444.70.0496090.5321100
2.44-2.554.60.0455950.5561100
2.55-2.694.70.046190.583199.8
2.69-2.864.70.0326040.664199.8
2.86-3.084.70.036050.701199.5
3.08-3.394.60.0256090.685199.8
3.39-3.884.50.0216080.754198.7
3.88-4.884.30.0195880.856195.6
4.88-3040.0185600.741186.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→25.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.367 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 567 4.8 %RANDOM
Rwork0.202 ---
obs0.203 11921 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.493 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 0 120 820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022720
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.951989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.571587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99523.82434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77315104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.85155
X-RAY DIFFRACTIONr_chiral_restr0.1270.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02565
X-RAY DIFFRACTIONr_nbd_refined0.2090.2267
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2494
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.214
X-RAY DIFFRACTIONr_mcbond_it1.1991.5461
X-RAY DIFFRACTIONr_mcangle_it2.0852741
X-RAY DIFFRACTIONr_scbond_it3.0913292
X-RAY DIFFRACTIONr_scangle_it5.2724.5248
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 40 -
Rwork0.419 795 -
obs-835 100 %

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