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- PDB-4qid: Crystal structure of Haloquadratum walsbyi bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 4qid
TitleCrystal structure of Haloquadratum walsbyi bacteriorhodopsin
ComponentsBacteriorhodopsin-I
KeywordsMEMBRANE PROTEIN / Bacteriorhodopsin / proton pump / membrane
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / 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
ACETATE ION / Chem-MPG / RETINAL / Bacteriorhodopsin-I
Similarity search - Component
Biological speciesHaloquadratum walsbyi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsWang, A.H.J. / Hsu, M.F. / Yang, C.S. / Fu, H.Y.
CitationJournal: To be Published
Title: An acid-tolerant light-driven proton pump
Authors: Wang, A.H.J. / Hsu, M.F. / Yang, C.S. / Fu, H.Y. / Cai, C.J. / Yi, H.P.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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: Bacteriorhodopsin-I
B: Bacteriorhodopsin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0247
Polymers56,9802
Non-polymers1,0445
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-27 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.939, 29.799, 124.973
Angle α, β, γ (deg.)90.00, 118.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriorhodopsin-I


Mass: 28490.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloquadratum walsbyi (archaea) / Strain: DSM 16790 / HBSQ001 / Gene: bop1, bopI, HQ_1014A / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: Q18DH8
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4
Details: ammonium sulfate, NaCl, sodium acetate, PEG 200, pH 4.0, LIPID CUBIC PHASE, temperature 293.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 20, 2013
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.57→30 Å / Num. obs: 48309 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 8.212
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.016 / Rsym value: 0.791 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→28.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.435 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.717 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 691 5 %RANDOM
Rwork0.20705 ---
obs0.20818 13107 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.988 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20.62 Å2
2---2.29 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.57→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 72 102 3661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023634
X-RAY DIFFRACTIONr_bond_other_d0.0020.023614
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9834949
X-RAY DIFFRACTIONr_angle_other_deg0.98638222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.175450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01322.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.1415558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8281518
X-RAY DIFFRACTIONr_chiral_restr0.1230.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024024
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02860
LS refinement shellResolution: 2.568→2.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 51 -
Rwork0.225 895 -
obs--94.04 %

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