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- PDB-4x32: Bacteriorhodopsin ground state structure collected in cryo condit... -

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Basic information

Entry
Database: PDB / ID: 4x32
TitleBacteriorhodopsin ground state structure collected in cryo conditions from crystals obtained in LCP with PEG as a precipitant.
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / light-driven proton pump / retinal binding / seven transmembrane helix protein
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
Chem-LI1 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsNogly, P. / Standfuss, J.
CitationJournal: Iucrj / Year: 2015
Title: Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.
Authors: Nogly, P. / James, D. / Wang, D. / White, T.A. / Zatsepin, N. / Shilova, A. / Nelson, G. / Liu, H. / Johansson, L. / Heymann, M. / Jaeger, K. / Metz, M. / Wickstrand, C. / Wu, W. / Bath, P. ...Authors: Nogly, P. / James, D. / Wang, D. / White, T.A. / Zatsepin, N. / Shilova, A. / Nelson, G. / Liu, H. / Johansson, L. / Heymann, M. / Jaeger, K. / Metz, M. / Wickstrand, C. / Wu, W. / Bath, P. / Berntsen, P. / Oberthuer, D. / Panneels, V. / Cherezov, V. / Chapman, H. / Schertler, G. / Neutze, R. / Spence, J. / Moraes, I. / Burghammer, M. / Standfuss, J. / Weierstall, U.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,38810
Polymers24,9911
Non-polymers5,3979
Water54030
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,16430
Polymers74,9723
Non-polymers16,19227
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-y+2,x-y-1,z1
crystal symmetry operation3_875-x+y+3,-x+2,z1
Buried area19060 Å2
ΔGint-167 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.525, 60.525, 101.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bacteriorhodopsin / / BR / Bacterioopsin / BO


Mass: 24990.535 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 18-245 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: ATCC 700922 / JCM 11081 / NRC-1 / Tissue: purple membrane / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / 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.: 8 / Source method: obtained synthetically / Formula: C42H86O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Description: hexagonal plate with 50 microns in the longest dimension
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 5.6 / Details: 27% PEG2000, 100 mM phosphate buffer pH 5.6 / PH range: 5.4-5.8

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream of LN2
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 274871 / Rmerge(I) obs: 0.107 / Χ2: 1.06 / D res high: 1.79 Å / Num. obs: 19786 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
5.3446.5778310.026
3.795.34135410.04
3.13.79176010.065
2.683.1207610.135
2.42.68232010.252
2.192.4258310.462
2.032.19281310.839
1.92.03299211.637
1.791.9310512.562
ReflectionResolution: 1.9→46.57 Å / Num. all: 16647 / Num. obs: 16643 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 33.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.026 / Net I/σ(I): 17.9 / Num. measured all: 234541
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.9414.31.8671.81531410720.5480.496100
9.11-46.5712.90.02168.6211716410.00699.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.49 Å46.57 Å
Translation5.49 Å46.57 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NTU

2ntu


Resolution: 1.9→52.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.283 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 841 5.1 %RANDOM
Rwork0.1715 15773 --
obs0.1737 15773 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.4 Å2 / Biso mean: 36.741 Å2 / Biso min: 22.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0.51 Å2-0 Å2
2---1.03 Å2-0 Å2
3---3.33 Å2
Refinement stepCycle: final / Resolution: 1.9→52.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 124 30 1864
Biso mean--53.95 47.85 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021889
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221934
X-RAY DIFFRACTIONr_angle_refined_deg1.2232.0082550
X-RAY DIFFRACTIONr_angle_other_deg0.7682.9764422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6465224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88822.28157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70615271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.915156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0221965
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022412
X-RAY DIFFRACTIONr_mcbond_it1.3482.555893
X-RAY DIFFRACTIONr_mcbond_other1.3492.555892
X-RAY DIFFRACTIONr_mcangle_it1.923.8191115
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 60 -
Rwork0.217 1164 -
all-1224 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 85.0075 Å / Origin y: 32.9867 Å / Origin z: -4.5054 Å
111213212223313233
T0.0626 Å2-0.0013 Å2-0.0143 Å2-0.0437 Å20.0364 Å2--0.0377 Å2
L1.9658 °20.0113 °20.0193 °2-1.3191 °20.1814 °2--0.6192 °2
S-0.0222 Å °0.2233 Å °0.2193 Å °-0.1244 Å °0.0299 Å °0.1034 Å °-0.0474 Å °-0.0247 Å °-0.0078 Å °

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