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- PDB-8w7r: H. walsbyi bacteriorhodopsin mutant - W94F -

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Basic information

Entry
Database: PDB / ID: 8w7r
TitleH. walsbyi bacteriorhodopsin mutant - W94F
ComponentsBacteriorhodopsin-I
KeywordsMEMBRANE PROTEIN / bacteriorhodopsin / light-driven proton pump
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
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin-I
Similarity search - Component
Biological speciesHaloquadratum walsbyi DSM 16790 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsLi, G.Y. / Chen, J.C. / Yang, C.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Not funded Taiwan
CitationJournal: To Be Published
Title: Crystal structure of H. walsbyi bacteriorhodopsin mutant - W94F at 2.38 Angstroms resolution.
Authors: Li, G.Y. / Chen, J.C. / Yang, C.S.
History
DepositionAug 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)59,67813
Polymers56,9022
Non-polymers2,77611
Water46826
1
B: Bacteriorhodopsin-I
hetero molecules

A: Bacteriorhodopsin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,67813
Polymers56,9022
Non-polymers2,77611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4890 Å2
ΔGint-32 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.499, 126.747, 55.037
Angle α, β, γ (deg.)90.000, 111.442, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 11 - 239 / Label seq-ID: 11 - 239

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bacteriorhodopsin-I / HwBR / Squarebop I


Mass: 28451.053 Da / Num. of mol.: 2 / Mutation: W94F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloquadratum walsbyi DSM 16790 (archaea)
Gene: bop1, bopI, HQ_1014A / Production host: Escherichia coli (E. coli) / References: UniProt: Q18DH8

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5 / Details: 50mM Sodium acetate, 50mM NaCl, 15% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→28.581 Å / Num. obs: 21677 / % possible obs: 99.61 % / Redundancy: 3.1 % / Biso Wilson estimate: 41.15 Å2 / Rrim(I) all: 0.097 / Net I/σ(I): 14.22
Reflection shellResolution: 2.5→2.64 Å / Mean I/σ(I) obs: 2.14 / Num. unique obs: 3427 / CC1/2: 0.73 / Rrim(I) all: 0.724 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.503→26.96 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.202 / SU B: 9.088 / SU ML: 0.201 / Average fsc free: 0.9576 / Average fsc work: 0.9724 / Cross valid method: FREE R-VALUE / ESU R: 0.444 / ESU R Free: 0.279 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1085 5.01 %RANDOM
Rwork0.2127 20570 --
all0.215 ---
obs-21655 99.508 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.025 Å20 Å2-0.014 Å2
2---0.008 Å2-0 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 2.503→26.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 191 26 3737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123787
X-RAY DIFFRACTIONr_angle_refined_deg1.41.7845114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0725458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.916542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25810567
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.87510130
X-RAY DIFFRACTIONr_chiral_restr0.1160.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022718
X-RAY DIFFRACTIONr_nbd_refined0.2170.21883
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2113
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.21
X-RAY DIFFRACTIONr_mcbond_it3.1884.131841
X-RAY DIFFRACTIONr_mcangle_it4.6377.3892295
X-RAY DIFFRACTIONr_scbond_it4.5674.6391946
X-RAY DIFFRACTIONr_scangle_it6.8558.3242819
X-RAY DIFFRACTIONr_lrange_it8.41247.3265927
X-RAY DIFFRACTIONr_ncsr_local_group_10.0430.057770
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.04340.05009
12AX-RAY DIFFRACTIONLocal ncs0.04340.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.503-2.5680.247770.2414670.24115740.960.96198.0940.221
2.568-2.6380.301780.24214950.24515740.9490.96199.93650.218
2.638-2.7130.271760.22214240.22415020.960.96999.86680.195
2.713-2.7960.225730.20313920.20414650.970.9741000.175
2.796-2.8870.32710.21413400.21814150.9390.97499.71730.183
2.887-2.9870.301670.21612990.2213670.9430.97199.92680.182
2.987-3.0980.276690.21812870.2213570.9450.97199.92630.184
3.098-3.2230.278630.20211980.20612630.960.97799.84170.175
3.223-3.3640.316610.2111460.21512110.9380.97399.66970.184
3.364-3.5250.251590.211240.20211880.9640.97699.57910.177
3.525-3.7120.228550.20110590.20311180.9710.97899.64220.185
3.712-3.9330.227530.20610230.20710810.9630.97499.53750.192
3.933-4.1980.262500.2279380.2299890.9630.97399.89890.223
4.198-4.5250.242480.2378940.2379460.9640.96799.57720.234
4.525-4.9430.281420.2138170.2158600.950.97699.88370.21
4.943-5.5040.298390.27430.2057820.9580.9791000.199
5.504-6.3120.226350.2486430.2466800.9710.97699.70590.235
6.312-7.6260.227300.2015610.2025920.9780.98499.83110.196
7.626-10.3780.163240.1294470.134780.9860.99298.53560.144
10.378-26.960.253150.2432730.2443040.9630.97294.73680.267

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