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- PDB-3vvk: An M-like Reaction State of the azide-bound purple form of pharao... -

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Basic information

Entry
Database: PDB / ID: 3vvk
TitleAn M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / seven-transmembrane-retinylidene protein / chloride-bound purple form / light-driven chloride ion pump / azide-bound purple form / light-driven proton pump
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 / AZIDE ION / Chem-L3P / RETINAL / Halorhodopsin / :
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKouyama, T. / Nakanishi, T.
CitationJournal: Biophys.J. / Year: 2013
Title: Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide
Authors: Nakanishi, T. / Kanada, S. / Murakami, M. / Ihara, K. / Kouyama, T.
History
DepositionJul 26, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Halorhodopsin
B: Halorhodopsin
C: Halorhodopsin
D: Halorhodopsin
E: Halorhodopsin
F: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,93225
Polymers185,8516
Non-polymers8,08119
Water5,134285
1
A: Halorhodopsin
B: Halorhodopsin
C: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,20912
Polymers92,9253
Non-polymers4,2849
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Halorhodopsin
E: Halorhodopsin
F: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,72313
Polymers92,9253
Non-polymers3,79710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.850, 97.900, 101.020
Angle α, β, γ (deg.)90.00, 128.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 10 molecules ABCDEF

#1: Protein
Halorhodopsin


Mass: 30975.096 Da / Num. of mol.: 6 / 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
#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

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Non-polymers , 5 types, 300 molecules

#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical ChemComp-22B / BACTERIORUBERIN


Mass: 741.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H76O4
#5: Chemical
ChemComp-L3P / 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE


Mass: 885.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C46H94O11P2
#6: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 1.6 Å3/Da / Density % sol: 23.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5 mg/ml nonyl glucoside, 2.7M ammonium sulfate, 0.16M NaCl, 0.1M HEPES, 0.04% NaN3 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2011 / Details: mirrors
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→79 Å / Num. all: 52756 / Num. obs: 48183 / % possible obs: 92.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.3-2.423.70.3483.5279470.34899.8
7.27-79.033.30.05718.654590.05797.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a7k

3a7k


Resolution: 2.3→15 Å / Occupancy max: 1 / Occupancy min: 0.36 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE POLYPEPTIDE CHAINS A, B AND C REPRESENT THE REACTION STATES TRAPED IN THE THREE SUBUNITS WITHIN THE ASYMMETRIC UNIT WHEN THE C2 CRYSTAL OF THE HALORHODOPSIN-AZIDE COMPLEX WAS FLASH- ...Details: THE POLYPEPTIDE CHAINS A, B AND C REPRESENT THE REACTION STATES TRAPED IN THE THREE SUBUNITS WITHIN THE ASYMMETRIC UNIT WHEN THE C2 CRYSTAL OF THE HALORHODOPSIN-AZIDE COMPLEX WAS FLASH-COOLED UNDER THE ILLUMINATION WITH ORANGE LIGHT, WHILE THE CHAINS D, E AND F REPRESENT THE UNPHOTOLYSED STATES.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2409 -RANDOM
Rwork0.2109 ---
all-51929 --
obs-48009 92.5 %-
Solvent computationBsol: 75.1402 Å2
Displacement parametersBiso max: 77.46 Å2 / Biso mean: 26.524 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--2.453 Å20 Å2-10.803 Å2
2---0.429 Å20 Å2
3---2.882 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-6 Å
Luzzati sigma a0.19 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11769 0 347 285 12401
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1771.5
X-RAY DIFFRACTIONc_scbond_it1.7132
X-RAY DIFFRACTIONc_mcangle_it1.7792
X-RAY DIFFRACTIONc_scangle_it2.2562.5
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.2841 266 -
Rwork0.234 --
obs-4873 95 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5cis.param

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