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- PDB-4qry: the ground state and the N intermediate of pharaonis halorhodopsi... -

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Basic information

Entry
Database: PDB / ID: 4qry
Titlethe ground state and the N intermediate of pharaonis halorhodopsin in complex with bromide ion
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / 7 transmembrane helices / light-driven chloride ion pump / retinal bacterioruberin / membrane
Function / homologyRhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / BROMIDE ION / 2,3-DI-PHYTANYL-GLYCEROL / RETINAL / :
Function and homology information
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKouyama, T. / Kawaguchi, H.
CitationJournal: Biophys.J. / Year: 2015
Title: Crystal Structures of the L1, L2, N, and O States of pharaonis Halorhodopsin
Authors: Kouyama, T. / Kawaguchi, H. / Nakanishi, T. / Kubo, H. / Murakami, M.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: 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
E: Halorhodopsin
F: Halorhodopsin
G: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,96735
Polymers185,8516
Non-polymers8,11629
Water5,188288
1
A: Halorhodopsin
B: Halorhodopsin
C: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,52415
Polymers92,9253
Non-polymers2,59912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Halorhodopsin
F: Halorhodopsin
G: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,44320
Polymers92,9253
Non-polymers5,51817
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.360, 98.300, 100.530
Angle α, β, γ (deg.)90.00, 128.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 11 molecules ABCEFG

#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
#4: 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.: 5
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 , 4 types, 312 molecules

#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br
#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.: 6 / Source method: obtained synthetically / Formula: C43H88O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 23.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6
Details: The C2 crystal of halorhodopsin grew when a solution containing 3 mg/ml halorhodopsin, 0.4 % nonylglucoside, 1 M ammonium sulfate, 0.16 M sodium chloride, 0.04 M sodium citrate at pH 6 and 0. ...Details: The C2 crystal of halorhodopsin grew when a solution containing 3 mg/ml halorhodopsin, 0.4 % nonylglucoside, 1 M ammonium sulfate, 0.16 M sodium chloride, 0.04 M sodium citrate at pH 6 and 0.04 % sodium azide was concentrated by the vapor diffusion using a reservoir solution containing 2.8 M ammonium sulfate and 0.12 M sodium citrate at pH 6. For investigation of light-induced structural changes, the C2 crystal was soaked in a solution containing 0.1 M sodium bromide, 1.5 M trisodium citrate at pH 7 and 30 % trehalose. This crystal was illuminated at 240 K with orange light and cooled to 100 K at a rate of 2.3 K/sec in the dark., VAPOR DIFFUSION, SITTING DROP, temperature 278K

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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: Jun 3, 2014
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: 2.2→49.13 Å / Num. all: 59552 / Num. obs: 58957 / % possible obs: 99 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 3.2 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8518 / Rsym value: 0.5 / % possible all: 98.5

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Processing

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

3qbk


Resolution: 2.2→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE THREE CHAINS (A B AND C) REPRESENT THE REACTION STATES THAT WERE GENERATED BY ILLUMINATION AT 240 K AND REMAINED TRAPPED AFTER SLOW COOLING TO 100K IN THE DARK. THE OTHER THREE CHAINS (E ...Details: THE THREE CHAINS (A B AND C) REPRESENT THE REACTION STATES THAT WERE GENERATED BY ILLUMINATION AT 240 K AND REMAINED TRAPPED AFTER SLOW COOLING TO 100K IN THE DARK. THE OTHER THREE CHAINS (E F AND G) REPRESENT THE UNPHOTOLYZED STATES THAT CO-EXISTED IN THE ILLUMINATED CRYSTAL. THE ASYMMETRIC UNIT OF THE C2 CRYSTAL CONTAINS THREE SUBUNITS. THESE THREE SUBUNITS UNDERWENT DIFFERENT STRUCTURAL CHANGES WHEN THE CRYSTAL WAS ILLUMINATED AT 240K. THE C2 CRYSTAL HAD BEEN SOAKED IN 0.1M SODIUM BROMIDE, 1.5M TRISODIUM-CITRATE AT pH 7 AND 30% TREHALOSE. THE DIFFRACTION DATA WERE COLLECTED AFTER THE ILLUMINATED CRYSTAL WAS COOLED TO 100 K WITH A RATE 2.3K/SEC IN THE DARK.
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 2967 -RANDOM
Rwork0.214 ---
obs0.214 58744 98.9 %-
all-59422 --
Displacement parametersBiso mean: 24.9699 Å2
Baniso -1Baniso -2Baniso -3
1-0.976 Å20 Å22.474 Å2
2--3.066 Å20 Å2
3----4.042 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-6 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11759 0 357 288 12404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_d1.22
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.8

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