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- PDB-3a7k: Crystal structure of halorhodopsin from Natronomonas pharaonis -

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Basic information

Entry
Database: PDB / ID: 3a7k
TitleCrystal structure of halorhodopsin from Natronomonas pharaonis
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / Light-driven chloride ion pump / Trimeric Bacterioruberin-Protein Complex / Retinal Protein
Function / homology
Function and homology information


Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BACTERIORUBERIN / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 2,3-DI-PHYTANYL-GLYCEROL / Chem-L3P / RETINAL / :
Similarity search - Component
Biological speciesNatronomonas pharaonis DSM 2160 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKouyama, T.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis.
Authors: Kouyama, T. / Kanada, S. / Takeguchi, Y. / Narusawa, A. / Murakami, M. / Ihara, K.
History
DepositionSep 27, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Halorhodopsin
B: Halorhodopsin
D: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,30033
Polymers92,9253
Non-polymers17,37430
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-56 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.830, 99.770, 99.270
Angle α, β, γ (deg.)90.00, 127.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABD

#1: Protein Halorhodopsin


Mass: 30975.096 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: STRAIN MK-1 WAS A HALORHODOPSIN-OVERPRODUCING MUTANT GENERATED FROM TYPE STRAIN D2160T.
Source: (natural) Natronomonas pharaonis DSM 2160 (archaea) / References: UniProt: Q3ITX1

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Non-polymers , 7 types, 174 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-22B / BACTERIORUBERIN


Mass: 741.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C50H76O4
#4: Chemical ChemComp-L1P / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCERO-3-PHOSPHATE


Mass: 733.137 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H89O6P
#5: Chemical
ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C43H88O3
#6: Chemical
ChemComp-L3P / 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE


Mass: 885.179 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C46H94O11P2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: A DROP CONTAINING 1MG/ML PROTEIN, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, 0.04% NAN2, 5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVE SOLUTION ...Details: A DROP CONTAINING 1MG/ML PROTEIN, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, 0.04% NAN2, 5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVE SOLUTION CONTAINING 2.6 M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, PH 8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→60.1 Å / Num. obs: 79092 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / Rsym value: 0.556 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1e12

1e12


Resolution: 2→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3975 -RANDOM
Rwork0.249 ---
all-78925 --
obs-78528 99.6 %-
Solvent computationBsol: 109.866 Å2
Displacement parametersBiso mean: 49.222 Å2
Baniso -1Baniso -2Baniso -3
1-2.094 Å20 Å2-12.748 Å2
2--2.659 Å20 Å2
3----4.754 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5868 0 666 144 6678
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_scbond_it1.7172
X-RAY DIFFRACTIONc_mcangle_it1.8952
X-RAY DIFFRACTIONc_scangle_it2.3942.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDTotal num. of bins used
2-2.070.36753850.348X-RAY DIFFRACTION6
2.07-2.150.33953880.3168X-RAY DIFFRACTION6
2.15-2.250.32714200.2908X-RAY DIFFRACTION6
2.25-2.370.29613870.2735X-RAY DIFFRACTION6
2.37-2.520.31974100.2732X-RAY DIFFRACTION6
2.52-2.710.28324010.251X-RAY DIFFRACTION6
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ret.param
X-RAY DIFFRACTION5CNS_TOPPAR:ion.param

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