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- PDB-6xl3: Mastigocladopsis repens rhodopsin chloride pump -

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Basic information

Entry
Database: PDB / ID: 6xl3
TitleMastigocladopsis repens rhodopsin chloride pump
ComponentsMastigocladopsis repens rhodopsin chloride pump
KeywordsMEMBRANE PROTEIN / retinal protein / proton pump / ion pump
Function / homologyTETRADECANE / DECANE / RETINAL
Function and homology information
Biological speciesMastigocladopsis repens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsBesaw, J.E. / Ernst, O.P. / Ou, W. / Morizumi, T.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants.
Authors: Besaw, J.E. / Ou, W.L. / Morizumi, T. / Eger, B.T. / Sanchez Vasquez, J.D. / Chu, J.H.Y. / Harris, A. / Brown, L.S. / Miller, R.J.D. / Ernst, O.P.
History
DepositionJun 28, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionJul 29, 2020ID: 6NWF
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.pdbx_database_id_DOI ..._chem_comp.pdbx_synonyms / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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: Mastigocladopsis repens rhodopsin chloride pump
B: Mastigocladopsis repens rhodopsin chloride pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,77011
Polymers54,2632
Non-polymers1,5079
Water81145
1
A: Mastigocladopsis repens rhodopsin chloride pump
hetero molecules

A: Mastigocladopsis repens rhodopsin chloride pump
hetero molecules

A: Mastigocladopsis repens rhodopsin chloride pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,52921
Polymers81,3953
Non-polymers3,13318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11350 Å2
ΔGint-144 kcal/mol
Surface area25610 Å2
MethodPISA
2
B: Mastigocladopsis repens rhodopsin chloride pump
hetero molecules

B: Mastigocladopsis repens rhodopsin chloride pump
hetero molecules

B: Mastigocladopsis repens rhodopsin chloride pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,78212
Polymers81,3953
Non-polymers1,3879
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7640 Å2
ΔGint-56 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.911, 108.911, 116.074
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Mastigocladopsis repens rhodopsin chloride pump


Mass: 27131.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mastigocladopsis repens (bacteria) / Production host: Escherichia coli (E. coli)
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 53 molecules

#2: Chemical ChemComp-RET / RETINAL


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30
#6: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 307.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 3.6 M sodium phosphate monobasic monohydrate, pH 4.0, 180 mM 1,6 hexanediol, 3.5% triethylene glycol
PH range: 4.0 - 4.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.33→27.64 Å / Num. obs: 34069 / % possible obs: 99.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 35.1 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.6
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3344 / CC1/2: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IUAZ

Resolution: 2.33→27.64 Å / SU ML: 0.233 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.4762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 1995 5.86 %
Rwork0.2076 32035 -
obs0.2083 34030 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.62 Å2
Refinement stepCycle: LAST / Resolution: 2.33→27.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 93 45 3674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793731
X-RAY DIFFRACTIONf_angle_d1.00655087
X-RAY DIFFRACTIONf_chiral_restr0.3694589
X-RAY DIFFRACTIONf_plane_restr0.0055608
X-RAY DIFFRACTIONf_dihedral_angle_d18.67571286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.390.31031380.25862252X-RAY DIFFRACTION99.38
2.39-2.460.27281470.23942282X-RAY DIFFRACTION99.92
2.46-2.530.22821440.22742296X-RAY DIFFRACTION99.84
2.53-2.610.24081410.21122263X-RAY DIFFRACTION99.92
2.61-2.70.21161410.19412295X-RAY DIFFRACTION99.8
2.7-2.810.22521390.19272255X-RAY DIFFRACTION99.83
2.81-2.940.20431470.19592312X-RAY DIFFRACTION99.72
2.94-3.090.20021430.19112266X-RAY DIFFRACTION99.59
3.09-3.290.21931440.19482283X-RAY DIFFRACTION99.51
3.29-3.540.22081410.20592261X-RAY DIFFRACTION97.64
3.54-3.90.20881440.20252303X-RAY DIFFRACTION98.99
3.9-4.460.2051400.19832285X-RAY DIFFRACTION98.74
4.46-5.610.22341440.21212319X-RAY DIFFRACTION98.28
5.61-27.640.22181420.22282363X-RAY DIFFRACTION95.76

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