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- PDB-5g2a: The crystal structure of light-driven chloride pump ClR at pH 6.0... -

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Basic information

Entry
Database: PDB / ID: 5g2a
TitleThe crystal structure of light-driven chloride pump ClR at pH 6.0 with Bromide ion.
ComponentsCHLORIDE PUMPING RHODOPSIN
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


photoreceptor activity / phototransduction / membrane
Similarity search - Function
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
BROMIDE ION / RETINAL / Chloride pumping rhodopsin
Similarity search - Component
Biological speciesNONLABENS MARINUS S1-08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)30,9344
Polymers30,4901
Non-polymers4443
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.774, 48.850, 69.363
Angle α, β, γ (deg.)90.00, 110.13, 90.00
Int Tables number5
Space group name H-MC121

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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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.68 Å3/Da / Density % sol: 54.12 % / 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: 0.9197
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 17312 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 35.45
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.26 / % possible all: 98.8

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Processing

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

3x3b


Resolution: 2.17→65.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.802 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20714 823 4.8 %RANDOM
Rwork0.15313 ---
obs0.15583 16316 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.47 Å2
2--3.99 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.17→65.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 22 59 2153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022145
X-RAY DIFFRACTIONr_bond_other_d0.0020.022090
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9492923
X-RAY DIFFRACTIONr_angle_other_deg1.12634759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5485263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.46923.82781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66815342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.765155
X-RAY DIFFRACTIONr_chiral_restr0.1260.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022403
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02528
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_it2.7122.6331055
X-RAY DIFFRACTIONr_mcbond_other2.7042.631054
X-RAY DIFFRACTIONr_mcangle_it2.7683.9391317
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9393.081090
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_restr4.39334232
X-RAY DIFFRACTIONr_sphericity_free19.155525
X-RAY DIFFRACTIONr_sphericity_bonded7.0454217
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 54 -
Rwork0.181 1167 -
obs--96.6 %

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