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- PDB-2ii9: Anabaena sensory rhodopsin transducer -

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Basic information

Entry
Database: PDB / ID: 2ii9
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
B: Sensory rhodopsin transducer protein
C: Sensory rhodopsin transducer protein
D: Sensory rhodopsin transducer protein


Theoretical massNumber of molelcules
Total (without water)58,8174
Polymers58,8174
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-35 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.152, 78.842, 70.582
Angle α, β, γ (deg.)90.000, 106.810, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPROAA2 - 173 - 18
21LEULEUPROPROBB2 - 173 - 18
31LEULEUPROPROCC2 - 173 - 18
41LEULEUPROPRODD2 - 173 - 18
52VALVALVALVALAA33 - 10134 - 102
62VALVALVALVALBB33 - 10134 - 102
72VALVALVALVALCC33 - 10134 - 102
82VALVALVALVALDD33 - 10134 - 102

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Components

#1: Protein
Sensory rhodopsin transducer protein


Mass: 14704.335 Da / Num. of mol.: 4
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.: 201 / 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: 1.93 Å3/Da / Density % sol: 36.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM Na2HPO4, 100 mM citric acid, 35% (v/v) 2-propanol, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1
DetectorDetector: CCD / Date: May 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 29903 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.081 / Χ2: 0.759 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.072.30.35728000.69292.9
2.07-2.152.70.31629090.67797.3
2.15-2.2530.2829760.74599.1
2.25-2.373.30.25830080.71599.9
2.37-2.523.40.21330300.659100
2.52-2.713.50.15130160.669100
2.71-2.993.50.10129930.687100
2.99-3.423.50.0630550.749100
3.42-4.33.60.04430220.977100
4.3-283.50.03230940.947100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.23 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.683 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2774 10 %RANDOM
Rwork0.215 ---
obs0.22 27875 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: 21.898 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.04 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→28.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 0 201 3109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222990
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9544105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28623.768138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54215434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.321520
X-RAY DIFFRACTIONr_chiral_restr0.1190.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022336
X-RAY DIFFRACTIONr_nbd_refined0.2160.21155
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3860.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3570.226
X-RAY DIFFRACTIONr_mcbond_it1.4361.51931
X-RAY DIFFRACTIONr_mcangle_it2.28623081
X-RAY DIFFRACTIONr_scbond_it3.07331216
X-RAY DIFFRACTIONr_scangle_it5.094.51024
Refine LS restraints NCS

Ens-ID: 1 / Number: 665 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.080.05
2BTIGHT POSITIONAL0.090.05
3CTIGHT POSITIONAL0.090.05
4DTIGHT POSITIONAL0.110.05
1ATIGHT THERMAL0.270.5
2BTIGHT THERMAL0.290.5
3CTIGHT THERMAL0.280.5
4DTIGHT THERMAL0.290.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 173 -
Rwork0.24 1564 -
obs-1737 100 %

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