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- PDB-4x31: Room temperature structure of bacteriorhodopsin from lipidic cubi... -

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Basic information

Entry
Database: PDB / ID: 4x31
TitleRoom temperature structure of bacteriorhodopsin from lipidic cubic phase obtained with serial millisecond crystallography using synchrotron radiation
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / light-driven proton pump / seven transmembrane helix protein / room temperature structure / retinal-binding protein
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 / molecular replacement / Resolution: 2.4 Å
AuthorsNogly, P. / James, D. / Wang, D. / White, T. / Zatsepin, N. / Shilova, A. / Nelson, G. / Liu, H. / Johansson, L. / Heymann, M. ...Nogly, P. / James, D. / Wang, D. / White, T. / Zatsepin, N. / Shilova, A. / Nelson, G. / Liu, H. / Johansson, L. / Heymann, M. / Jaeger, K. / Metz, M. / Wickstrand, C. / Wu, W. / Baath, P. / Berntsen, P. / Oberthuer, D. / Panneels, V. / Cherezov, V. / Chapman, H. / Spence, J. / Schertler, G. / Neutze, R. / Moraes, I. / Burghammer, M. / Standfuss, J. / Weierstall, U.
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
Revision 1.4Oct 23, 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: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5427
Polymers25,0621
Non-polymers3,4806
Water18010
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,62521
Polymers75,1853
Non-polymers10,44018
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 area14460 Å2
ΔGint-166 kcal/mol
Surface area26100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.790, 62.790, 109.670
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: 25061.615 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 18-246 / 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


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.: 5 / Source method: obtained synthetically / Formula: C42H86O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Description: thin plate microcrystals, 5-40 microns in the longest dimension
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 5.6
Details: Precipitant: 27%-39% PEG 2000, 100 mM phosphate buffer pH 5.6. MAG 9.9 used for LCP formation. Crystallization setup in Hamilton syringe with tube of LCP surrounded by precipitant.
PH range: 5.4-5.8

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Data collection

DiffractionMean temperature: 294 K
Ambient temp details: ambient room temperature in the experimental hutch at ID13 ESRF
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→36.56 Å / Num. all: 9655 / Num. obs: 9655 / % possible obs: 100 % / Redundancy: 127 % / Rsym value: 0.224 / Net I/σ(I): 3.57
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 88.8 % / Mean I/σ(I) obs: 1.16 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å31.4 Å
Translation2.8 Å31.4 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H68

1h68


Resolution: 2.4→31.4 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 23.607 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.507 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 441 4.6 %RANDOM
Rwork0.2053 9192 --
obs0.2072 9633 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.09 Å2 / Biso mean: 58.52 Å2 / Biso min: 37.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å21.14 Å2-0 Å2
2--2.28 Å20 Å2
3----7.4 Å2
Refinement stepCycle: final / Resolution: 2.4→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 82 10 1848
Biso mean--69.15 55.94 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021882
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211896
X-RAY DIFFRACTIONr_angle_refined_deg1.0131.9972549
X-RAY DIFFRACTIONr_angle_other_deg0.7492.9864331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.545228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91422.28157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7715277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.673156
X-RAY DIFFRACTIONr_chiral_restr0.0520.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221998
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022415
X-RAY DIFFRACTIONr_mcbond_it1.4853.834915
X-RAY DIFFRACTIONr_mcbond_other1.4833.826914
X-RAY DIFFRACTIONr_mcangle_it2.6735.7361142
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 30 -
Rwork0.307 682 -
all-712 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.133 Å / Origin y: 39.552 Å / Origin z: 35.717 Å
111213212223313233
T0.0298 Å2-0.0104 Å2-0.0365 Å2-0.0265 Å2-0.0107 Å2--0.4594 Å2
L1.5495 °2-0.1577 °2-0.447 °2-2.3964 °2-0.2146 °2--1.2824 °2
S-0.0364 Å °-0.0863 Å °0.0222 Å °0.2317 Å °-0.0096 Å °-0.1325 Å °-0.0978 Å °0.1805 Å °0.046 Å °

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