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- PDB-1e12: Halorhodopsin, a light-driven chloride pump -

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Basic information

Entry
Database: PDB / ID: 1000000000000
TitleHalorhodopsin, a light-driven chloride pump
ComponentsHALORHODOPSIN
KeywordsTRANSPORT PROTEIN / ION PUMP / CHLORIDE PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PALMITATE / HALOARCHAEA / CHLORIDE TRANSPORT
Function / homology
Function and homology information


photoreceptor activity / phototransduction / monoatomic ion channel activity / 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
: / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / RETINAL / Halorhodopsin
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEssen, L.-O. / Kolbe, M. / Oesterhelt, D.
Citation
Journal: Science / Year: 2000
Title: Structure of Light-Driven Chloride Pump Halorhodopsin at 1.8 A Resolution
Authors: Kolbe, M. / Besir, H. / Essen, L.-O. / Oesterhelt, D.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1998
Title: The Structure and Mechanism of the Family of Retinal Proteins from Halophilic Archaea
Authors: Oesterhelt, D.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: Three-Dimensional Structure of Halorhodopsin at 7 Angstrom Resolution
Authors: Havelka, W. / Henderson, R. / Oesterhelt, D.
History
DepositionApr 14, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2000Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Feb 3, 2016Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Revision 1.3May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HALORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,12715
Polymers26,9471
Non-polymers4,18114
Water1,72996
1
A: HALORHODOPSIN
hetero molecules

A: HALORHODOPSIN
hetero molecules

A: HALORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,38245
Polymers80,8403
Non-polymers12,54242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area7970 Å2
ΔGint-135.6 kcal/mol
Surface area46150 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.300, 67.300, 209.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2019-

HOH

21A-2035-

HOH

31A-2086-

HOH

DetailsIN THE CRYSTALS, HR ASSEMBLES SIMILARLY TO HOMOTRIMERS AS BACTERIORHODOPSIN.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HALORHODOPSIN / HR


Mass: 26946.617 Da / Num. of mol.: 1 / Mutation: YES / Source method: isolated from a natural source
Details: H. SAL. STRAIN D2 WAS CONSTRUCTED FOR HOMOLOGOUS OVEREXPRESSION OF HR. SEE ALSO HEYMANN ET AL., MOL. MICROBIOL., VO. 7, 623-630 (1993).
Source: (natural) HALOBACTERIUM SALINARUM (Halophile) / Cellular location: MEMBRANE / Strain: D2 / References: UniProt: P0DMH7

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Non-polymers , 6 types, 110 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN A ENGINEERED MUTATION VAL229ALA
Has protein modificationY
Sequence detailsALA A 229, MUTATION IN D2 STRAIN VERIFIED BY DIDEOXY-SEQUENCING C-TERMINUS NOT DEFINED IN ELECTRON ...ALA A 229, MUTATION IN D2 STRAIN VERIFIED BY DIDEOXY-SEQUENCING C-TERMINUS NOT DEFINED IN ELECTRON DENSITY FROM A263 - D274. IN THE CRYSTALS, HR ASSEMBLES SIMILARLY TO HOMOTRIMERS AS BACTERIORHODOPSIN.

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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: 2.54 Å3/Da / Density % sol: 41.5 %
Crystal growMethod: lipidic cubic phase / pH: 7
Details: CRYSTALLIZED IN A CUBIC LIPID PHASE MADE OF 58-62 W/V % 1-MONOOLEIN, 4 M KCL, 3.3-4.0 MG/ML HR AND 50 MM TRIS/HCL, PH 7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 26590 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.8 / % possible all: 92.3
Reflection shell
*PLUS
% possible obs: 92.3 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRR

1brr


Resolution: 1.8→25 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: LIPID PATCH BETWEEN HR TRIMERS MODELLED WITH 1-MONOOLEIN MOLECULES. NOTE THAT THESE OLC MOLECULES ARE MOSTLY ONLY PARTIALLY DEFINED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1617 6 %RANDOM
Rwork0.237 ---
obs0.237 26513 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.897 Å2 / ksol: 0.332776 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.578 Å2-0.275 Å20 Å2
2---3.578 Å20 Å2
3---7.156 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 280 96 2169
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018721
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.77549
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.561.5
X-RAY DIFFRACTIONc_mcangle_it0.972
X-RAY DIFFRACTIONc_scbond_it0.692
X-RAY DIFFRACTIONc_scangle_it1.082.5
LS refinement shellResolution: 1.8→1.82 Å / Total num. of bins used: 32 /
RfactorNum. reflection
Rfree0.309 33
Rwork0.336 723
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1HR_DEPOSIT_PARAM.PROHR_DEPOSIT_TOP.PRO
X-RAY DIFFRACTION2PROTEIN.PARAMPROTEIN.TOP

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