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- PDB-1vgo: Crystal Structure of Archaerhodopsin-2 -

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Basic information

Entry
Database: PDB / ID: 1vgo
TitleCrystal Structure of Archaerhodopsin-2
ComponentsArchaerhodopsin 2
KeywordsPROTON TRANSPORT / retinal-binding protein
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
RETINAL / Archaerhodopsin-2
Similarity search - Component
Biological speciesHalobacterium sp. (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYoshimura, K. / Enami, N. / Murakami, M. / Okumura, H. / Ihara, K. / Kouyama, T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structures of archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps
Authors: Enami, N. / Yoshimura, K. / Murakami, M. / Okumura, H. / Ihara, K. / Kouyama, T.
History
DepositionApr 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _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 1.4Oct 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
B: Archaerhodopsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,15919
Polymers54,6262
Non-polymers4,53417
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-41 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.880, 139.480, 108.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Archaerhodopsin 2 / / AR 2


Mass: 27312.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Halobacterium sp. (Halophile) / Strain: aus-2 / References: UniProt: P29563
#2: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 4.24 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: ammonium sulfate, sodium chloride, nonyl glucoside, sodium citrate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→120 Å / Num. obs: 30865 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 63.7 Å2 / Limit h max: 48 / Limit h min: 0 / Limit k max: 55 / Limit k min: 0 / Limit l max: 42 / Limit l min: 0 / Observed criterion F max: 1136552.6 / Observed criterion F min: 6.3 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2970 / Rsym value: 0.493 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uaz

1uaz


Resolution: 2.5→14.94 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1313 4.9 %RANDOM
Rwork0.241 ---
all-32271 --
obs-26954 83.5 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 69.2908 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 158.28 Å2 / Biso mean: 61.85 Å2 / Biso min: 33.72 Å2
Baniso -1Baniso -2Baniso -3
1--5.62 Å20 Å20 Å2
2---3.72 Å20 Å2
3---9.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 307 29 3956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.3621644.80.33532600.0283956342486.5
2.61-2.750.311724.90.28133700.0243990354288.7
2.75-2.920.2681554.40.24533870.0214030354287.9
2.92-3.140.2617550.23533300.023999350587.6
3.14-3.460.2661714.90.22533140.024037348586.3
3.46-3.950.2571425.50.24524590.0224025260164.6
3.95-4.950.281704.90.23432850.0214079345584.7
4.95-14.940.2461644.80.23432360.0194184340081.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5so4.param

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