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- PDB-3nsb: Structure of bacteriorhodopsin ground state before and after X-ra... -

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Basic information

Entry
Database: PDB / ID: 3nsb
TitleStructure of bacteriorhodopsin ground state before and after X-ray modification
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / ION PUMP / RETINAL PROTEIN / PHOTORECEPTOR / MEROHEDRAL TWINNING / radiation damage / 7-helix transmembrane / ion transport / Membrane
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / 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
Chem-LI1 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBorshchevskiy, V.I.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: X-ray-Radiation-Induced Changes in Bacteriorhodopsin Structure.
Authors: Borshchevskiy, V.I. / Round, E.S. / Popov, A.N. / Buldt, G. / Gordeliy, V.I.
History
DepositionJul 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 1.3Nov 20, 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: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,85111
Polymers26,8141
Non-polymers6,03710
Water70339
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,55333
Polymers80,4433
Non-polymers18,11030
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 area13990 Å2
ΔGint-189 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.995, 60.995, 109.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bacteriorhodopsin / BR


Mass: 26814.412 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 14-261 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: S9 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-LI1 / 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL / LIPID FRAGMENT


Mass: 639.130 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C42H86O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / pH: 5.6
Details: monoolein meso phase, K/Na-Pi as a precipitant, pH 5.6, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2005
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.78→30.1 Å / Num. obs: 22171 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.058 / Net I/σ(I): 20.3
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.539 / % possible all: 99.6

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Processing

Software
NameClassification
DNAdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3W

1c3w


Resolution: 1.78→30.1 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE DATA USED FOR THIS REFINEMENT WERE COLLECTED FROM A CRYSTAL WITH MEROHEDRAL TWINNING RATIO OF 62:38. THE DATA WERE DETWINNED PRIOR TO REFINEMENT. MODEL REFINED AS TWO CONFORMATIONS: "A", ...Details: THE DATA USED FOR THIS REFINEMENT WERE COLLECTED FROM A CRYSTAL WITH MEROHEDRAL TWINNING RATIO OF 62:38. THE DATA WERE DETWINNED PRIOR TO REFINEMENT. MODEL REFINED AS TWO CONFORMATIONS: "A", THE STATE BEFORE X-RAY MODIFICATION (PDB ENTRY 3NS0), WAS FIXED DURING REFINEMENT. "B" WITH 35% OCCUPANCY, THE BR STRUCTURE AFTER X-RAY MODIFICATION, WAS REFINED.
RfactorNum. reflectionSelection details
Rfree0.225 997 RANDOM
Rwork0.209 --
obs0.209 19842 -
all-19842 -
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å2--
2---2.24 Å2-
3---4.48 Å2
Refinement stepCycle: LAST / Resolution: 1.78→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 88 39 1852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
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_deg2.06
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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