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- PDB-2ei4: Trimeric complex of archaerhodopsin-2 -

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Basic information

Entry
Database: PDB / ID: 2ei4
TitleTrimeric complex of archaerhodopsin-2
ComponentsArchaerhodopsin-2
KeywordsTRANSPORT PROTEIN / membrane protein / retinal / bacterioruberin / proton pump / Structural Genomics
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / 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
BACTERIORUBERIN / alpha-D-glucopyranose / 2,3-DI-PHYTANYL-GLYCEROL / RETINAL / Archaerhodopsin-2
Similarity search - Component
Biological speciesHalobacterium sp. AUS-2 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKouyama, T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2
Authors: Yoshimura, K. / Kouyama, T.
History
DepositionMar 11, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1725
Polymers27,3131
Non-polymers1,8594
Water19811
1
A: Archaerhodopsin-2
hetero molecules

A: Archaerhodopsin-2
hetero molecules

A: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,51515
Polymers81,9383
Non-polymers5,57712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area18130 Å2
ΔGint-119 kcal/mol
Surface area24990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.160, 98.160, 56.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Archaerhodopsin-2 / AR 2


Mass: 27312.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium sp. AUS-2 (Halophile) / Strain: aus-2 / References: UniProt: P29563
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 14 molecules

#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical ChemComp-22B / BACTERIORUBERIN


Mass: 741.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H76O4
#5: Chemical ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H88O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.8M ammonium sulfate, 0.1M HEPES, 0.32% nonylglucoside, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2006
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 18116 / Num. obs: 18116 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 30.359 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.085 / Net I/σ(I): 6.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2669 / Rsym value: 0.484 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXL-97model building
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1vgo

1vgo


Resolution: 2.1→15 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The crystal was hemihedrally twinned. The twinning fraction was estimated to be 43-45%. After averaging the twin-related intensities, the refinement was performed by the detwin_perfect procedure of cns.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1651 -RANDOM
Rwork0.188 ---
all0.188 18468 --
obs-16803 91 %-
Displacement parametersBiso mean: 35.7301 Å2
Baniso -1Baniso -2Baniso -3
1-0.013 Å2-0.02 Å20 Å2
2--0.013 Å20 Å2
3----0.025 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 131 11 1980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005817
X-RAY DIFFRACTIONc_angle_deg1.10792
X-RAY DIFFRACTIONc_dihedral_angle_d17.65711
X-RAY DIFFRACTIONc_improper_angle_d0.72944
LS refinement shellResolution: 2.1→2.17 Å
RfactorNum. reflection% reflection
Rfree0.1875 168 -
Rwork0.1965 --
obs-1482 90.2 %

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