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- PDB-5azd: Crystal structure of thermophilic rhodopsin. -

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Basic information

Entry
Database: PDB / ID: 5azd
TitleCrystal structure of thermophilic rhodopsin.
ComponentsBacteriorhodopsin
KeywordsTRANSPORT PROTEIN / Membrane protein / Retinal / Ion pump / Thermal stability
Function / homology
Function and homology information


: / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020
Similarity search - Function
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
Biological speciesThermus thermophilus JL-18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMizutani, K. / Hashimoto, N. / Tsukamoto, T. / Yamashita, K. / Yamamoto, M. / Sudo, Y. / Murata, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: To Be Published
Title: X-ray crystallographic structure of thermophilic rhodopsin: implications for high thermal stability and optogenetic availability.
Authors: Tsukamoto, T. / Mizutani, K. / Hasegawa, T. / Takahashi, M. / Hashimoto, N. / Shimono, K. / Yamashita, K. / Yamamoto, M. / Miyauchi, S. / Takagi, S. / Hayashi, S. / Sudo, Y. / Murata, T.
History
DepositionSep 30, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
B: Bacteriorhodopsin
C: Bacteriorhodopsin
D: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)121,2314
Polymers121,2314
Non-polymers00
Water362
1
A: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)30,3081
Polymers30,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)30,3081
Polymers30,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)30,3081
Polymers30,3081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)30,3081
Polymers30,3081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-74 kcal/mol
Surface area41170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.186, 67.693, 73.045
Angle α, β, γ (deg.)116.48, 114.14, 90.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bacteriorhodopsin / / thermophilic rhodopsin


Mass: 30307.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus JL-18 (bacteria) / Gene: TtJL18_1346 / Plasmid: pKI81 / Details (production host): pBAD derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9ZSC3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal growTemperature: 296 K / Method: lipidic cubic phase / pH: 3.6 / Details: 100mM sodium citrate pH3.6, 34% PEG 400 (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 30, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→46.52 Å / Num. all: 22129 / Num. obs: 22122 / % possible obs: 93.19 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.1192 / Net I/σ(I): 6.26
Reflection shellResolution: 2.796→2.896 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4538 / Mean I/σ(I) obs: 1.77 / % possible all: 89.08

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DDL

3ddl


Resolution: 2.8→46.519 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 1123 5.1 %Random selection
Rwork0.2284 ---
obs0.2311 22039 93.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→46.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7898 0 0 2 7900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038134
X-RAY DIFFRACTIONf_angle_d0.73711139
X-RAY DIFFRACTIONf_dihedral_angle_d16.7654788
X-RAY DIFFRACTIONf_chiral_restr0.0321281
X-RAY DIFFRACTIONf_plane_restr0.0041337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.92760.30561380.27842615X-RAY DIFFRACTION94
2.9276-3.08190.34781440.27892699X-RAY DIFFRACTION96
3.0819-3.2750.30591160.25632739X-RAY DIFFRACTION96
3.275-3.52770.30971510.2452726X-RAY DIFFRACTION97
3.5277-3.88260.27731600.2222671X-RAY DIFFRACTION97
3.8826-4.4440.2611380.20682579X-RAY DIFFRACTION95
4.444-5.59750.27691270.20682231X-RAY DIFFRACTION96
5.5975-46.52540.21651490.20092656X-RAY DIFFRACTION95
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)
11.6097-0.94970.44983.64290.07760.6379-0.1346-0.1020.06440.57510.2755-0.18930.28150.1858-0.17960.33310.06970.00650.31640.02150.138717.3065-69.08226.4154
22.34321.81891.75853.6419-0.20353.68250.0823-0.8785-0.3270.21010.3416-0.7155-0.32960.8565-0.77870.5231-0.0529-0.06020.3776-0.17550.454615.9685-50.562835.0529
32.46491.7351.46642.98830.08891.4399-0.31060.45040.02630.22690.2614-0.26610.11030.4230.1440.28820.115-0.02290.4012-0.1050.352333.0501-70.803113.8785
40.37090.00250.36871.46370.2140.7979-0.04830.11550.03990.0195-0.0069-0.09530.131-0.02970.00970.2799-0.02170.07020.2963-0.07830.289524.3111-66.7859.7893
50.3942-0.96420.28063.31730.85412.0166-0.1533-0.0813-0.0350.56720.25250.02620.13410.2153-0.0860.2184-0.01730.07770.2931-0.02780.259748.1048-66.613826.567
62.9976-0.37251.654.0889-1.50412.1474-0.2010.4016-0.10040.79980.0474-1.05320.07780.92760.2080.459-0.23180.12070.6047-0.20760.762854.5617-53.194732.1228
74.9257-0.6435-1.22120.908-1.21513.0217-0.0805-0.189-0.0421-0.3224-0.212-0.1276-0.36450.64270.01120.27220.06810.050.3934-0.01830.21960.8098-72.349613.1236
82.18650.1060.4511.8545-1.09120.7499-0.04250.1242-0.0548-0.2785-0.0432-0.30890.10220.36210.08230.30550.01130.07460.48720.08960.259863.6724-64.59245.6891
91.1784-0.79110.44891.3719-1.43371.96270.00040.14360.05610.00680.031-0.04210.37430.0623-0.03060.2777-0.0735-0.02020.2467-0.04360.272950.1834-67.035311.1068
101.04791.47281.34183.69381.50313.1488-0.16940.04260.0596-0.42640.10930.3995-0.65190.14840.10390.29270.0040.0550.2196-0.0150.29998.9963-73.534437.6513
110.1090.21990.46510.46170.73384.5567-0.47430.1906-0.30940.2534-0.04140.7341-0.1723-0.17470.11530.6056-0.0130.33780.4706-0.1310.68642.8221-61.95746.718
121.31520.1132-0.61670.77230.35944.1794-0.1544-0.0755-0.16370.12930.3722-0.30250.4607-0.856-0.16570.3005-0.0298-0.01080.4280.05670.3782-5.8152-89.223247.7471
131.12550.19570.44221.2897-0.79722.2101-0.037-0.0746-0.1265-0.2030.13460.02880.16840.0730.00950.27460.00290.03870.27010.03410.34877.0249-87.29844.7027
140.4960.53660.49672.7221.4511.7573-0.26210.02580.1073-0.27920.15450.65560.01510.05690.08830.3104-0.0557-0.08020.24550.09320.320540.58-73.290536.7331
150.08170.08750.65340.09330.69985.22890.09650.0315-0.21860.3963-0.07980.79670.0165-1.56060.32820.2635-0.00760.13210.62820.13760.799435.1427-59.874346.3313
161.4567-1.3971-2.12462.27621.53123.1855-0.2349-0.2496-0.1239-0.25940.08390.56-0.23090.03360.10770.2027-0.0464-0.09930.32020.00880.455223.8867-85.21645.8533
170.8135-1.2057-0.73752.59411.58831.86920.2452-0.0238-0.52020.1914-0.10420.03790.43720.1410.10870.7535-0.1153-0.02270.1516-0.150.438426.8448-105.346541.3128
180.6689-0.30190.03440.1242-0.04830.8952-0.0686-0.0547-0.0092-0.17270.2285-0.00740.13850.2066-0.1280.28-0.01840.04170.23550.06260.280537.3956-86.337844.0843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 140 )
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 253 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 91 )
7X-RAY DIFFRACTION7chain 'B' and (resid 92 through 114 )
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 180 )
9X-RAY DIFFRACTION9chain 'B' and (resid 181 through 252 )
10X-RAY DIFFRACTION10chain 'C' and (resid 4 through 82 )
11X-RAY DIFFRACTION11chain 'C' and (resid 83 through 91 )
12X-RAY DIFFRACTION12chain 'C' and (resid 92 through 179 )
13X-RAY DIFFRACTION13chain 'C' and (resid 180 through 254 )
14X-RAY DIFFRACTION14chain 'D' and (resid 4 through 82 )
15X-RAY DIFFRACTION15chain 'D' and (resid 83 through 89 )
16X-RAY DIFFRACTION16chain 'D' and (resid 90 through 167 )
17X-RAY DIFFRACTION17chain 'D' and (resid 168 through 180 )
18X-RAY DIFFRACTION18chain 'D' and (resid 181 through 253 )

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