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- PDB-2ii8: Anabaena sensory rhodopsin transducer -

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Basic information

Entry
Database: PDB / ID: 2ii8
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: 2.1 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: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
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: 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
Water10,485582
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 area5370 Å2
ΔGint-35 kcal/mol
Surface area18200 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
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-32 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.799, 119.236, 120.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H

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
11SERSERPROPROAA3 - 174 - 18
21SERSERPROPROBB3 - 174 - 18
31SERSERPROPROCC3 - 174 - 18
41SERSERPROPRODD3 - 174 - 18
51SERSERPROPROEE3 - 174 - 18
61SERSERPROPROFF3 - 174 - 18
71SERSERPROPROGG3 - 174 - 18
81SERSERPROPROHH3 - 174 - 18
92THRTHRGLNGLNAA32 - 10233 - 103
102THRTHRGLNGLNBB32 - 10233 - 103
112THRTHRGLNGLNCC32 - 10233 - 103
122THRTHRGLNGLNDD32 - 10233 - 103
132THRTHRGLNGLNEE32 - 10233 - 103
142THRTHRGLNGLNFF32 - 10233 - 103
152THRTHRGLNGLNGG32 - 10233 - 103
162THRTHRGLNGLNHH32 - 10233 - 103

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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 / Water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
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: ALS / Beamline: 4.2.2
DetectorDetector: CCD / Date: Apr 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 62002

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.22 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.011 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 4286 7.1 %RANDOM
Rwork0.228 ---
obs0.231 60426 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5943 0 0 582 6525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226114
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.958392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2275743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0523.846286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66815886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8221540
X-RAY DIFFRACTIONr_chiral_restr0.1420.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024790
X-RAY DIFFRACTIONr_nbd_refined0.2220.22599
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2539
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.210
X-RAY DIFFRACTIONr_mcbond_it1.4731.53941
X-RAY DIFFRACTIONr_mcangle_it2.29126293
X-RAY DIFFRACTIONr_scbond_it3.00832474
X-RAY DIFFRACTIONr_scangle_it4.9484.52099
Refine LS restraints NCS

Ens-ID: 1 / Number: 673 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.140.05
2BTIGHT POSITIONAL0.120.05
3CTIGHT POSITIONAL0.130.05
4DTIGHT POSITIONAL0.130.05
5ETIGHT POSITIONAL0.120.05
6FTIGHT POSITIONAL0.120.05
7GTIGHT POSITIONAL0.120.05
8HTIGHT POSITIONAL0.130.05
1ATIGHT THERMAL0.540.5
2BTIGHT THERMAL0.370.5
3CTIGHT THERMAL0.290.5
4DTIGHT THERMAL0.380.5
5ETIGHT THERMAL0.290.5
6FTIGHT THERMAL0.480.5
7GTIGHT THERMAL0.320.5
8HTIGHT THERMAL0.390.5
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 294 -
Rwork0.247 3881 -
obs-4175 92.82 %

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