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- PDB-1x0i: Crystal Structure of the Acid Blue Form of Bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 1x0i
TitleCrystal Structure of the Acid Blue Form of Bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / 7 transmembrane helices / membrane protein
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / monoatomic ion channel activity / proton transmembrane transport / 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
2,3-DI-PHYTANYL-GLYCEROL / Chem-L3P / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOkumura, H. / Murakami, M. / Kouyama, T.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of Acid Blue and Alkaline Purple Forms of Bacteriorhodopsin
Authors: Okumura, H. / Murakami, M. / Kouyama, T.
History
DepositionMar 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Other
Revision 1.4Oct 25, 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 1.5Oct 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
1: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5047
Polymers26,8141
Non-polymers3,6896
Water45025
1
1: Bacteriorhodopsin
hetero molecules

1: Bacteriorhodopsin
hetero molecules

1: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,51121
Polymers80,4433
Non-polymers11,06818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)102.640, 102.640, 109.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Number of models2

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Components

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Protein , 1 types, 1 molecules 1

#1: Protein Bacteriorhodopsin / BR


Mass: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: JW3 / References: UniProt: P02945

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Non-polymers , 5 types, 31 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#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.: 3 / Source method: obtained synthetically / Formula: C46H94O11P2
#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.: 1 / Source method: obtained synthetically / Formula: C43H88O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.09 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 2
Details: ammonium sulfate, pH 2.00, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Nov 28, 2004 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→54.52 Å / Num. all: 15620 / Num. obs: 15527 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 45 Å2 / Limit h max: 38 / Limit h min: 0 / Limit k max: 22 / Limit k min: 0 / Limit l max: 47 / Limit l min: 0 / Observed criterion F max: 2176769.36 / Observed criterion F min: 20.1 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2216 / Rsym value: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iw6

1iw6


Resolution: 2.3→14.91 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 767 4.9 %RANDOM
Rwork0.238 ---
all0.238 15587 --
obs0.238 15506 99.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 84.2683 Å2 / ksol: 0.413201 e/Å3
Displacement parametersBiso max: 158.02 Å2 / Biso mean: 43.54 Å2 / Biso min: 15.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å21.36 Å20 Å2
2--3.27 Å20 Å2
3----1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 133 25 1824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg1
X-RAY DIFFRACTIONx_torsion_impr_deg0.41
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.480.2731384.60.23628930.0233042303199.6
2.48-2.720.2811555.10.21428840.0233046303999.8
2.72-3.120.251434.60.20529420.0213092308599.8
3.12-3.910.261645.30.21729370.023108310199.8
3.91-14.910.3081675.10.26730830.0243302325098.4

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