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- PDB-5g28: The crystal structure of light-driven chloride pump ClR at pH 6.0. -

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Basic information

Entry
Database: PDB / ID: 5g28
TitleThe crystal structure of light-driven chloride pump ClR at pH 6.0.
ComponentsCHLORIDE PUMPING RHODOPSIN
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


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
OLEIC ACID / RETINAL / Chloride pumping rhodopsin
Similarity search - Component
Biological speciesNONLABENS MARINUS S1-08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsKim, K.L. / Kwon, S.K. / Jun, S.H. / Cha, J.S. / Kim, H.Y. / Kim, J.H. / Cho, H.S.
CitationJournal: Nat.Commun. / Year: 2016
Title: Crystal Structure and Functional Characterization of a Light-Driven Chloride Pump Having an Ntq Motif.
Authors: Kim, K. / Kwon, S. / Jun, S. / Cha, J.S. / Kim, H. / Lee, W. / Kim, J.F. / Cho, H.
History
DepositionApr 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Other
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 13, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHLORIDE PUMPING RHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,82211
Polymers30,4901
Non-polymers2,33310
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.756, 49.402, 69.327
Angle α, β, γ (deg.)90.00, 109.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2133-

HOH

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Components

#1: Protein CHLORIDE PUMPING RHODOPSIN / CHLORIDE PUMP RHODOPSIN


Mass: 30489.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NONLABENS MARINUS S1-08 (bacteria) / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W8VZW3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.76 Å3/Da / Density % sol: 55.44 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→65.21 Å / Num. obs: 45878 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 30.81
Reflection shellResolution: 1.57→1.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.58 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3X3B

3x3b


Resolution: 1.57→65.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.481 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19378 2168 4.9 %RANDOM
Rwork0.15399 ---
obs0.15594 42520 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.202 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.13 Å2
2--1.03 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.57→65.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 121 136 2329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022237
X-RAY DIFFRACTIONr_bond_other_d0.0020.022240
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.983013
X-RAY DIFFRACTIONr_angle_other_deg1.11135114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7715263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71223.82781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55515342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.098155
X-RAY DIFFRACTIONr_chiral_restr0.1450.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022450
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02542
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2051.8781055
X-RAY DIFFRACTIONr_mcbond_other2.1841.8741054
X-RAY DIFFRACTIONr_mcangle_it2.3742.7961317
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7532.4891182
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.68834471
X-RAY DIFFRACTIONr_sphericity_free26.965531
X-RAY DIFFRACTIONr_sphericity_bonded8.66454533
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 168 -
Rwork0.265 2961 -
obs--92.27 %

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