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- PDB-3abw: Crystal structure of pharaonis halorhodopsin in complex with azide ion -

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Basic information

Entry
Database: PDB / ID: 3abw
TitleCrystal structure of pharaonis halorhodopsin in complex with azide ion
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / LIGHT-DRIVEN CHLORIDE ION PUMP / TRIMERIC BACTERIORUBERIN-PROTEIN COMPLEX / RETINAL PROTEIN
Function / homologyRhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / BACTERIORUBERIN / AZIDE ION / Chem-L3P / RETINAL / :
Function and homology information
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKouyama, T. / Kanada, S.
CitationJournal: To be Published
Title: Binding mode of azide ion to pharaonis halorhodopsin
Authors: Kanada, S. / Kouyama, T.
History
DepositionDec 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: 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_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 1.3Oct 30, 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: Halorhodopsin
B: Halorhodopsin
D: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,35420
Polymers92,9253
Non-polymers10,42817
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-55 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.090, 98.790, 100.140
Angle α, β, γ (deg.)90.00, 127.85, 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 (archaea) / Strain: MK-1 / References: UniProt: Q3ITX1

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Non-polymers , 5 types, 145 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.: 2 / Source method: obtained synthetically / Formula: C50H76O4
#4: 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
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 61.52 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6
Details: A DROP CONTAINING 2MG/ML Halorhodopsin, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M Na-citrate, 0.04% NAN3,5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSIONAGAINST A RESERVE SOLUTION ...Details: A DROP CONTAINING 2MG/ML Halorhodopsin, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M Na-citrate, 0.04% NAN3,5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSIONAGAINST A RESERVE SOLUTION CONTAINING 2.9 M AMMONIUM SULFATE, 0.04M Na-citrate, PH 6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K. After the crystal grew, the mother solution was exchanged with a solution containing 3M Ammonium sulfate, 200 mM Na-N3, 100 mM HEPES (pH7) and 30 % trehalose.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 14, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38.15 Å / Num. all: 91795 / Num. obs: 80799 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 10.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.526 / % possible all: 74.3

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3a7k

3a7k


Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 4064 4.4 %RANDOM
Rwork0.2423 ---
all-91821 --
obs-80687 87.9 %-
Solvent computationBsol: 99.0968 Å2
Displacement parametersBiso mean: 32.4952 Å2
Baniso -1Baniso -2Baniso -3
1-2.914 Å20 Å2-9.532 Å2
2---1.368 Å20 Å2
3----1.546 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5889 0 303 128 6320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2391.5
X-RAY DIFFRACTIONc_mcangle_it1.8092
X-RAY DIFFRACTIONc_scbond_it1.8162
X-RAY DIFFRACTIONc_scangle_it2.4342.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
1.9-1.970.38542950.3718X-RAY DIFFRACTION
1.97-2.050.30144310.2786X-RAY DIFFRACTION
2.05-2.140.26863480.2673X-RAY DIFFRACTION
2.14-2.250.24623860.2409X-RAY DIFFRACTION
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4so4.param
X-RAY DIFFRACTION5tra.param
X-RAY DIFFRACTION6bru.param
X-RAY DIFFRACTION7l1p.param
X-RAY DIFFRACTION8l2p.param
X-RAY DIFFRACTION9l3p.param
X-RAY DIFFRACTION10azi.param

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