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- PDB-3qbk: Bromide-bound form of pharaonis halorhodopsin -

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Basic information

Entry
Database: PDB / ID: 3qbk
TitleBromide-bound form of pharaonis halorhodopsin
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / Retinal 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 / BROMIDE ION / RETINAL / Halorhodopsin / :
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Halorhodopsin
B: Halorhodopsin
D: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,74014
Polymers92,9253
Non-polymers2,81511
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-68 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.150, 99.720, 99.970
Angle α, β, γ (deg.)90.00, 127.80, 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


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-22B / BACTERIORUBERIN


Mass: 741.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H76O4
#4: Chemical
ChemComp-BR / BROMIDE ION


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


Mass: 18.015 Da / Num. of mol.: 151 / 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: 61.85 %
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: 0.1 M Sodium Bromide, 3 M ammonium sulfate, 0.1 ...Details: Crystallization: 3.5 mg/ml halorhodopsin, 5mg/ml nonylglucoside, 2.8M ammonium sulfate, 0.1 M glycine, 0.1M NaCl Post-crystallization soaking: 0.1 M Sodium Bromide, 3 M ammonium sulfate, 0.1 M Hepes (pH7), 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: 0.912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2010 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2.2→49.9 Å / Num. all: 59789 / Num. obs: 58115 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 5.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.5 / Num. unique all: 7213 / Rsym value: 0.501 / % possible all: 82.9

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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: 2.2→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 2936 -RANDOM
Rwork0.2482 ---
obs0.2482 58105 97.3 %-
Displacement parametersBiso mean: 38.4497 Å2
Baniso -1Baniso -2Baniso -3
1-9.8 Å20 Å27.737 Å2
2---10.139 Å20 Å2
3---0.332 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 120 151 6153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006409
X-RAY DIFFRACTIONc_angle_d1.13455
X-RAY DIFFRACTIONc_dihedral_angle_d18.61401
X-RAY DIFFRACTIONc_improper_angle_d0.79057
X-RAY DIFFRACTIONc_mcbond_it1.2341.5
X-RAY DIFFRACTIONc_scbond_it1.7322
X-RAY DIFFRACTIONc_mcangle_it1.8972
X-RAY DIFFRACTIONc_scangle_it2.3642.5
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 DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5tra.param

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