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- PDB-3qbg: Anion-free blue form of pharaonis halorhodopsin -

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Basic information

Entry
Database: PDB / ID: 3qbg
TitleAnion-free blue form of pharaonis halorhodopsin
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / ion pump / retinal / Membrane
Function / homology
Function and homology information


photoreceptor activity / phototransduction / 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 / RETINAL / Halorhodopsin / :
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKouyama, T. / Kanada, S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin
Authors: Kanada, S. / Takeguchi, Y. / Murakami, M. / Ihara, K. / Kouyama, T.
History
DepositionJan 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
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.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 1.3Nov 1, 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: Halorhodopsin
B: Halorhodopsin
D: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,48612
Polymers92,9253
Non-polymers3,5619
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-56 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.480, 97.820, 101.450
Angle α, β, γ (deg.)90.00, 128.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Halorhodopsin /


Mass: 30975.096 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: STRAIN MK-1 WAS A HALORHODOPSIN-OVERPRODUCING MUTANT GENERATED FROM TYPE STRAIN D2160T.
Source: (natural) Natronomonas pharaonis (archaea) / Strain: MK-1 / References: UniProt: Q3ITX1, UniProt: P15647*PLUS
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-22B / BACTERIORUBERIN / Halobacterium


Mass: 741.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H76O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Crystallization: 3.5 mg/ml halorhodopsin, 5mg/ml nonylglucoside, 2.8M ammonium sulfate, 0.1 M glycine, 0.1M NaCl Post-crystallization soaking: 3 M ammonium sulfate, 0.1 M glycine (pH9.3-- ...Details: Crystallization: 3.5 mg/ml halorhodopsin, 5mg/ml nonylglucoside, 2.8M ammonium sulfate, 0.1 M glycine, 0.1M NaCl Post-crystallization soaking: 3 M ammonium sulfate, 0.1 M glycine (pH9.3-->pH8), 30% trehalose, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2010 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.2 Å / Num. all: 108631 / Num. obs: 97036 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.083 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.8-1.93.60.632.114989195.7
1.9-2.010.391.6119561

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A7K

3a7k


Resolution: 1.8→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4861 -RANDOM
Rwork0.2281 ---
obs0.2281 96867 89.2 %-
all-108119 --
Displacement parametersBiso mean: 24.1076 Å2
Baniso -1Baniso -2Baniso -3
1-1.169 Å20 Å21.275 Å2
2--0.844 Å20 Å2
3----2.013 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-6 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 0 198 212 6307
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005476
X-RAY DIFFRACTIONc_angle_d1.11061
X-RAY DIFFRACTIONc_dihedral_angle_d18.1974
X-RAY DIFFRACTIONc_improper_angle_d0.77749
X-RAY DIFFRACTIONc_mcbond_it1.0851.5
X-RAY DIFFRACTIONc_scbond_it1.8082
X-RAY DIFFRACTIONc_mcangle_it1.6112
X-RAY DIFFRACTIONc_scangle_it2.5012.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4bng.param
X-RAY DIFFRACTION5tra.param

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