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- PDB-5ite: 2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi B... -

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Basic information

Entry
Database: PDB / ID: 5ite
Title2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR) from Octylglucoside (OG) Detergent Micelles
ComponentsBacteriorhodopsin-I
KeywordsMEMBRANE PROTEIN / bacteriorhodopsin from Haloquadratum walsbyi / lipidic cubic phase (LCP) / OG detergent micelle / traditional
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
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin-I
Similarity search - Component
Biological speciesHaloquadratum walsbyi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.182 Å
AuthorsBroecker, J. / Eger, B.T. / Ernst, O.P.
Funding support Canada, Germany, 2items
OrganizationGrant numberCountry
Government of CanadaCanada Excellence Research Chair Program Canada
German Research Foundation (DFG)BR 5124/1-1 Germany
CitationJournal: Structure / Year: 2017
Title: Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs.
Authors: Broecker, J. / Eger, B.T. / Ernst, O.P.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 27, 2023Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin-I
B: Bacteriorhodopsin-I
C: Bacteriorhodopsin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,36515
Polymers87,3023
Non-polymers4,06212
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-49 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.442, 61.565, 119.689
Angle α, β, γ (deg.)90.00, 116.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriorhodopsin-I / HwBR / Squarebop I


Mass: 29100.809 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloquadratum walsbyi (archaea) / Strain: DSM 16790 / HBSQ001 / Gene: bop1, bopI, HQ_1014A / Production host: Escherichia coli (E. coli) / References: UniProt: Q18DH8
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRET (retinal) is covalently bound to lysine (K224)

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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: 2.07 Å3/Da / Density % sol: 40.49 % / Description: small compact, hexagonal plate
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: 8% (v/v) Tacsimate, 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→47.51 Å / Num. obs: 35898 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.45 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.171 / Net I/av σ(I): 6 / Net I/σ(I): 6
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QI1

4qi1


Resolution: 2.182→47.506 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2893 1735 4.84 %
Rwork0.2594 --
obs0.2609 35862 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.182→47.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5277 0 285 69 5631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085738
X-RAY DIFFRACTIONf_angle_d1.3897778
X-RAY DIFFRACTIONf_dihedral_angle_d13.1032084
X-RAY DIFFRACTIONf_chiral_restr0.062922
X-RAY DIFFRACTIONf_plane_restr0.01934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1824-2.24660.32891410.28172820X-RAY DIFFRACTION100
2.2466-2.31910.30971230.26382880X-RAY DIFFRACTION99
2.3191-2.4020.3061250.25682821X-RAY DIFFRACTION99
2.402-2.49820.28971560.24772827X-RAY DIFFRACTION99
2.4982-2.61190.29611350.24012857X-RAY DIFFRACTION100
2.6119-2.74960.31151700.23832814X-RAY DIFFRACTION99
2.7496-2.92180.2851160.24392918X-RAY DIFFRACTION99
2.9218-3.14740.27351550.25462805X-RAY DIFFRACTION99
3.1474-3.4640.25431500.24482856X-RAY DIFFRACTION99
3.464-3.96510.32311360.25412843X-RAY DIFFRACTION98
3.9651-4.99470.25111610.26972788X-RAY DIFFRACTION97
4.9947-47.51760.32181670.29532898X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4829-0.48090.59161.5949-0.84710.78510.01410.11520.0817-0.2672-0.1538-0.13750.25880.2849-0.26090.1413-0.0338-0.04960.17690.0330.1157.0529-21.978232.9355
20.01990.0189-0.03380.0272-0.02460.06340.14290.57330.396-0.34530.0856-0.0387-0.12930.3651-0.0010.5669-0.10610.11970.5133-0.01270.48550.9365-17.08029.0612
31.25160.3092-0.30720.83560.04560.1920.1141-0.0510.11520.1175-0.073-0.1394-0.0131-0.01070.04550.1281-0.0091-0.01470.130.01560.1391-9.0666-29.913332.7376
40.67560.1807-0.190.5854-0.20170.5582-0.06970.0405-0.0935-0.0190.029-0.1150.25390.2177-0.06430.1190.04340.02010.1561-0.00830.1729-0.6866-35.367323.8163
50.5432-0.512-0.09650.647-0.07960.7130.02160.07270.0998-0.11970.06120.0274-0.3705-0.24760.24020.1563-0.004-0.00360.1582-0.01040.1577-29.38110.006726.9704
60.8193-0.01460.40890.3493-0.07680.62470.0931-0.050.0611-0.0905-0.00590.0670.05460.03490.0840.1446-0.0042-0.01020.12210.01940.1372-14.1191-8.291332.4434
70.8638-0.0158-0.00230.96950.24220.4321-0.08560.12220.1595-0.1721-0.1341-0.0749-0.190.2797-0.6240.11960.0033-0.010.14070.01870.1392-9.44320.772423.0826
81.4820.47040.90470.7493-0.04811.48540.0761-0.1743-0.00940.0096-0.0906-0.041-0.236-0.26330.09740.12130.0362-0.00860.06150.03250.1448-20.9693.711425.3696
90.70480.1339-0.32390.5357-0.0420.6891-0.01970.1429-0.2118-0.061-0.1972-0.1321-0.0942-0.3465-0.42490.1638-0.02060.03270.1191-0.01290.1216-29.5676-40.531926.4451
100.66540.1283-0.11060.45090.20140.5446-0.05580.066-0.1139-0.05550.0667-0.03-0.03220.06070.00290.0988-0.01380.00960.12-0.01410.1267-30.1749-23.369532.3092
110.25750.16950.32470.65180.40812.2853-0.019-0.0628-0.0467-0.0253-0.12420.1619-0.1007-0.5416-0.36220.0954-0.0165-0.030.14470.00110.1596-40.2636-23.722322.3883
120.692-0.3418-0.34950.2572-0.00510.7174-0.1571-0.07510.062-0.0421-0.00620.0433-0.09890.1676-0.44090.135-0.08330.01430.1965-0.04870.2324-37.116-35.115326.3475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 11:39)
2X-RAY DIFFRACTION2(chain A and resid 40:48)
3X-RAY DIFFRACTION3(chain A and resid 49:154)
4X-RAY DIFFRACTION4(chain A and resid 155:238)
5X-RAY DIFFRACTION5(chain B and resid 11:47)
6X-RAY DIFFRACTION6(chain B and resid 48:154)
7X-RAY DIFFRACTION7(chain B and resid 155:209)
8X-RAY DIFFRACTION8(chain B and resid 210:238)
9X-RAY DIFFRACTION9(chain C and resid 11:47)
10X-RAY DIFFRACTION10(chain C and resid 48:154)
11X-RAY DIFFRACTION11(chain C and resid 155:207)
12X-RAY DIFFRACTION12(chain C and resid 208:238)

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