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- PDB-2ntw: Bacteriorhodopsin, wild type, after illumination to produce the L... -

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Basic information

Entry
Database: PDB / ID: 2ntw
TitleBacteriorhodopsin, wild type, after illumination to produce the L intermediate
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / SERPENTINE / ION TRANSPORT / PHOTOINTERMEDIATE
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / 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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsLanyi, J.K. / Schobert, B.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural changes in the L photointermediate of bacteriorhodopsin.
Authors: Lanyi, J.K. / Schobert, B.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2142
Polymers26,9301
Non-polymers2841
Water41423
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6426
Polymers80,7893
Non-polymers8533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6390 Å2
ΔGint-51 kcal/mol
Surface area25580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.966, 60.966, 110.388
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Number of models2

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Components

#1: Protein Bacteriorhodopsin / / BR


Mass: 26929.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANECell membrane / Gene: bop / Plasmid: PBA2 / Cellular location (production host): CYTOPLASM / Production host: Halobacterium salinarum (Halophile) / Strain (production host): MPK409 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


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


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 295 K / pH: 5.6
Details: MO:WATER:PHOSPHATE, PH 5.6, CUBIC LIPID PHASE, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97977
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Apr 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97977 Å / Relative weight: 1
ReflectionResolution: 1.53→25 Å / Num. all: 34929 / Num. obs: 33922 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 42.4
Reflection shellResolution: 1.53→1.59 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3333 / % possible all: 86.5

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3W

1c3w


Resolution: 1.53→25 Å / Num. parameters: 7056 / Num. restraintsaints: 20914 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: MODEL REFINED AS TWO CONFORMATIONS, "A" THE L STATE, "B" WITH 40% OCCUPANCY IS THE BR STATE. CONFORMATION BEFORE ILLUMINATION (PDB ENTRY 2NTU)
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1845 5 %RANDOM
all0.153 34929 --
obs0.153 33922 96.9 %-
Refine analyzeNum. disordered residues: 246 / Occupancy sum non hydrogen: 1763
Refinement stepCycle: LAST / Resolution: 1.53→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 20 23 1763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.588
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 1.53→1.59 Å / Num. reflection obs: 3333

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