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

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Basic information

Entry
Database: PDB / ID: 5itc
Title2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR) from Styrene Maleic Acid (SMA) Polymer Nanodiscs
ComponentsBacteriorhodopsin-I
KeywordsMEMBRANE PROTEIN / bacteriorhodopsin from Haloquadratum walsbyi / lipidic cubic phase / styrene maleic acid (SMA) polymer nanodisc / detergent-free
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 / molecular replacement / Resolution: 1.999 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 1.2Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)92,37616
Polymers87,9573
Non-polymers4,41913
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-51 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.715, 61.586, 119.089
Angle α, β, γ (deg.)90.00, 116.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 29318.961 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) / Strain (production host): C43(DE3) / References: UniProt: Q18DH8
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


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


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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 Å3/Da / Density % sol: 38.45 % / Description: big, flat hexagonal plate
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.8
Details: 1.6 M NH4PO4, 0.1 M NaCl, 0.2 M NaSCN, 0.016% amino acid mix (L-His, L-Leu, L-Ile, L-Trp, L-Tyr, and L-Phe in 0.2 M HEPES Na pH 6.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 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: 1.999→33.426 Å / Num. obs: 47014 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.17 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.197 / Net I/av σ(I): 6.3 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.999-2.053.20.693194.5
8.93-33.433.30.157198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4qi1


Resolution: 1.999→33.426 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 2298 4.89 %random
Rwork0.1996 ---
obs0.2016 47014 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→33.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5277 0 310 161 5748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155796
X-RAY DIFFRACTIONf_angle_d1.747861
X-RAY DIFFRACTIONf_dihedral_angle_d13.2172131
X-RAY DIFFRACTIONf_chiral_restr0.093932
X-RAY DIFFRACTIONf_plane_restr0.013945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9988-2.04220.33521320.25712679X-RAY DIFFRACTION96
2.0422-2.08970.27451440.22822786X-RAY DIFFRACTION100
2.0897-2.1420.27211280.20132807X-RAY DIFFRACTION100
2.142-2.19990.24821280.19692809X-RAY DIFFRACTION100
2.1999-2.26460.23381450.18112757X-RAY DIFFRACTION100
2.2646-2.33770.19961440.17992769X-RAY DIFFRACTION100
2.3377-2.42120.24051720.18262766X-RAY DIFFRACTION100
2.4212-2.51810.22441330.17912791X-RAY DIFFRACTION100
2.5181-2.63270.22991430.17942802X-RAY DIFFRACTION100
2.6327-2.77140.23831310.18272808X-RAY DIFFRACTION100
2.7714-2.9450.21821480.19272815X-RAY DIFFRACTION100
2.945-3.17220.24961360.20532800X-RAY DIFFRACTION100
3.1722-3.49110.24591660.19522774X-RAY DIFFRACTION100
3.4911-3.99560.2421480.19962828X-RAY DIFFRACTION100
3.9956-5.03120.22161580.20632819X-RAY DIFFRACTION100
5.0312-33.43050.2431420.21842906X-RAY DIFFRACTION100
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)
10.96560.2135-0.2140.7225-0.07370.9561-0.0358-0.07390.0677-0.0499-0.0441-0.0105-0.3547-0.1582-0.01940.126-0.00520.02510.1596-0.02470.138647.2159-8.6318139.6997
22.1414-0.29480.07060.73270.33940.18530.1720.4141-0.6196-0.4424-0.13960.40820.4801-0.68380.01340.439-0.0765-0.00590.43920.02960.323453.3344-13.6332115.7816
30.48810.1550.35690.07560.10720.26120.02920.0054-0.02470.0214-0.00610.0181-0.0040.034300.16650.0024-0.00440.1848-0.01140.188663.3454-0.9188139.3351
41.12880.5490.24071.07340.09430.3552-0.06430.03340.0183-0.02250.0460.0668-0.1795-0.2068-00.19360.0478-0.02080.2055-0.00790.216654.86714.6097130.1981
51.246-0.63240.45851.11390.0660.28160.02630.11290.0064-0.18840.03080.01280.28830.1507-0.00040.17750.00230.00140.16470.0170.203483.4621-30.8678133.8043
60.2987-0.03690.13790.24120.05080.75660.0334-0.0047-0.0382-0.0327-0.0479-0.06390.0545-0.028700.19080.00480.01040.177-0.00330.173268.2443-22.494139.2892
71.1669-0.1838-0.23341.0349-0.27920.26890.01320.177-0.0444-0.079-0.04520.0175-0.0048-0.0747-0.00030.2004-0.02880.0070.2033-0.01240.21363.6837-31.5873130.0042
80.58190.0157-0.03560.51530.00451.23760.0178-0.1146-0.00520.02130.00910.06830.4150.30470.09330.1740.00360.04480.0981-0.00840.098275.0982-34.5999132.1757
90.85530.2666-0.26671.54230.70770.50260.00540.09860.0321-0.0989-0.09430.05040.1950.008-0.00030.1595-0.02-0.01850.1720.00660.179483.8379.5848132.7509
100.47090.08650.11980.328-0.01480.7488-0.01420.01560.0501-0.03660.0148-0.0050.06810.0197-00.1681-0.0094-0.00040.18140.01190.173284.532-7.5174139.12
110.2976-0.0860.29641.0317-0.61910.5605-0.03680.05380.0262-0.1498-0.1251-0.113-0.00290.2483-0.00010.1721-0.00540.010.22490.00120.212894.6344-7.0658128.3904
120.7332-0.5671-0.0530.92670.35890.2062-0.02190.0304-0.01870.04970.0040.0187-0.20820.37490.00010.1836-0.0590.00160.23860.03380.233891.59574.1483133.0874
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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