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- PDB-3qbl: Pharaonis halorhodopsin complexed with nitrate -

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Basic information

Entry
Database: PDB / ID: 3qbl
TitlePharaonis halorhodopsin complexed with nitrate
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / Retinal protein / ion 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 / NITRATE 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: To be Published
Title: Crystal structures of anion-free blue and yellow forms 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 1.1Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,63314
Polymers92,9253
Non-polymers2,70811
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-58 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.750, 100.030, 99.330
Angle α, β, γ (deg.)90.00, 127.23, 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-22B / BACTERIORUBERIN


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
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: 0.4 M Sodium Nitrate, 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: 0.4 M Sodium Nitrate, 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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 59477 / Num. obs: 57277 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / Num. unique all: 7058 / Rsym value: 0.531 / % possible all: 96.3

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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
Rfree0.267 2885 -RANDOM
Rwork0.252 ---
obs0.262 57097 96.1 %-
all-59414 --
Displacement parametersBiso mean: 39.2004 Å2
Baniso -1Baniso -2Baniso -3
1-6.999 Å20 Å210.939 Å2
2---8.239 Å20 Å2
3---1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 138 136 6151
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006704
X-RAY DIFFRACTIONc_angle_d1.16316
X-RAY DIFFRACTIONc_dihedral_angle_d18.593
X-RAY DIFFRACTIONc_improper_angle_d0.79991

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