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- PDB-4gyc: Structure of the SRII(D75N mutant)/HtrII Complex in I212121 space... -

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Basic information

Entry
Database: PDB / ID: 4gyc
TitleStructure of the SRII(D75N mutant)/HtrII Complex in I212121 space group ("U" shape)
Components
  • Sensory rhodopsin II transducer
  • Sensory rhodopsin-2
KeywordsMEMBRANE PROTEIN / Photoreceptor
Function / homology
Function and homology information


photoreceptor activity / phototransduction / transmembrane signaling receptor activity / chemotaxis / lysozyme activity / monoatomic ion channel activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Htr2, transmembrane domain / Htr2 transmembrane domain / Helix hairpin bin / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain ...Htr2, transmembrane domain / Htr2 transmembrane domain / Helix hairpin bin / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / Bacterial rhodopsins retinal binding site. / HAMP domain profile. / HAMP domain / 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 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EICOSANE / RETINAL / Sensory rhodopsin-2 / Sensory rhodopsin II transducer
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0501 Å
AuthorsIshchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J. / Remeeva, A. / Utrobin, P. / Balandin, T. / Engelhard, M. ...Ishchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J. / Remeeva, A. / Utrobin, P. / Balandin, T. / Engelhard, M. / Bueldt, G. / Gordeliy, V.
CitationJournal: J Photochem Photobiol B / Year: 2013
Title: Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer.
Authors: Ishchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J.P. / Balandin, T. / Remeeva, A. / Engelhard, M. / Buldt, G. / Gordeliy, V.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Structure summary
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,95212
Polymers40,1252
Non-polymers2,82710
Water1,04558
1
A: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
hetero molecules

A: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,90424
Polymers80,2494
Non-polymers5,65520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556-x+1/2,y,-z+11
Buried area5840 Å2
ΔGint-70 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.465, 113.674, 126.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Sensory rhodopsin-2 / Sensory rhodopsin II / SR-II


Mass: 26196.711 Da / Num. of mol.: 1 / Mutation: D75N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: sop2, sopII / Production host: Escherichia coli (E. coli) / References: UniProt: P42196
#2: Protein Sensory rhodopsin II transducer / HTR-II / Methyl-accepting phototaxis protein II / MPP-II


Mass: 13927.909 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: htr2, htrII / Production host: Escherichia coli (E. coli) / References: UniProt: P42259
#3: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C20H42
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 295.5 K / Method: lipidic cubic phase / pH: 5.1
Details: 1M Na/KPi, 0.3M trehalose, pH 5.1, Lipidic cubic phase, temperature 295.5K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF ID23-120.934
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDOct 27, 2011
ADSC QUANTUM 315r2CCDFeb 6, 2010
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.0501→42.229 Å / Num. obs: 22785 / % possible obs: 99.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shellResolution: 2.0501→2.12 Å / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2S

1h2s


Resolution: 2.0501→42.229 Å / SU ML: 0.21 / σ(F): 1.17 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 1134 5 %RANDOM
Rwork0.2026 ---
obs0.2037 22783 99.26 %-
all-22783 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0501→42.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 102 58 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112196
X-RAY DIFFRACTIONf_angle_d1.132971
X-RAY DIFFRACTIONf_dihedral_angle_d14.791753
X-RAY DIFFRACTIONf_chiral_restr0.294361
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.12340.31092230.2714035X-RAY DIFFRACTION99
2.1234-2.20840.28192250.23984091X-RAY DIFFRACTION100
2.2084-2.30890.24251920.22414045X-RAY DIFFRACTION100
2.3089-2.43060.22982070.20164111X-RAY DIFFRACTION99
2.4306-2.58290.2142210.18944075X-RAY DIFFRACTION100
2.5829-2.78230.1972190.17524061X-RAY DIFFRACTION99
2.7823-3.06220.18032400.18734070X-RAY DIFFRACTION99
3.0622-3.50510.21282000.18554081X-RAY DIFFRACTION99
3.5051-4.41530.21352120.19274067X-RAY DIFFRACTION99
4.4153-42.23770.24062010.21794026X-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)
15.0921-2.3211-3.3096.0678-0.64213.4294-0.0855-0.34030.43460.3549-0.0177-0.4731-0.26840.3630.03790.3651-0.1097-0.07670.26390.01840.173911.166513.17842.0525
20.6554-0.3584-0.09291.86350.55091.6619-0.18260.0404-0.0191-0.2235-0.0628-0.19240.02640.23520.04260.1737-0.0146-0.0050.28670.04620.092411.5554-0.299537.9863
32.54181.26621.97064.3937-1.81123.59990.28370.1606-0.00270.0407-0.0509-0.142-0.38950.2676-0.2960.42260.06030.41410.24130.1266-0.254112.6417-10.924835.3822
41.0547-1.036-2.35214.14-0.36447.5049-0.74710.0968-1.32130.3956-0.26260.46120.7384-0.4330.99420.74670.25960.1670.4926-0.19520.5798.2763-19.685334.6349
53.5119-3.0371-1.56435.49-0.03414.6558-0.1980.2296-0.4132-0.2939-0.13850.24310.7919-0.42660.24120.3977-0.00970.06320.2525-0.00990.11932.7677-12.577337.0594
61.04960.2260.0671.2216-0.18731.4095-0.06470.22420.181-0.0217-0.05570.1053-0.32080.16140.07480.222-0.0348-0.06160.20220.03230.12413.27359.782337.0947
77.8602-4.3756-2.33915.67760.21257.4809-0.0454-0.47030.38040.42980.14410.0785-0.3263-0.0807-0.04030.61780.1475-0.03890.08140.03030.748-5.119321.453246.5097
80.81420.7194-0.1351.4344-1.03271.0674-0.13350.06330.27640.1171-0.0529-0.0621-0.19420.11020.10860.22370.0222-0.09170.15820.0290.2368-2.60758.165142.6884
91.0215-0.6595-0.20671.7272-1.12831.2639-0.15430.14440.0008-0.2535-0.01280.24390.1647-0.15670.14470.1464-0.0114-0.01940.1523-0.02190.1045-3.9145-7.909742.6808
107.7855-3.4702-0.58072.2256-0.19080.3353-0.00090.34770.2922-0.27520.03080.1863-0.1434-0.5045-0.01220.548-0.1442-0.07920.25710.02910.513-11.5197-16.623645.5699
111.330.130.20330.74880.10850.81630.04230.17190.07060.0313-0.02110.20550.0364-0.3386-0.02640.01270.101-0.18610.2205-0.06440.4247-11.90640.654246.5058
121.27090.87510.5352.5853-1.78612.564-0.05570.12120.37170.0364-0.01540.2345-0.3728-0.278-0.00450.34930.2629-0.12620.1983-0.14390.746-13.780615.568151.8798
131.96631.212-1.49436.35021.37742.3445-0.07290.09010.0226-0.0516-0.10240.4632-0.1349-0.57080.0467-0.19120.09060.1310.237-0.08570.3788-12.26590.833954.9631
142.796-3.2294-1.16478.02472.45032.5127-0.164-0.0121-0.5003-0.0005-0.06510.69860.6156-0.26440.21940.247-0.01860.04070.14250.01640.2461-6.8461-17.810853.962
152.7509-3.2705-2.08919.24322.07625.8716-0.0284-0.2579-0.38730.3137-0.2073-0.45530.24930.35040.130.17680.01550.10.22280.08030.20462.7856-17.956952.6528
161.14140.39310.41480.94190.07451.4536-0.0397-0.14340.15360.1656-0.09060.3632-0.1923-0.02660.13240.11380.01150.01460.1266-0.04280.1293-1.50982.85454.9455
170.4772-0.5530.2862.32620.48851.3182-0.08280.05940.3105-0.142-0.18920.1581-0.1754-0.04540.17880.2381-0.0178-0.05680.1435-0.02460.14924.662514.766552.8001
180.1681-0.184-0.09161.9157-0.03680.1889-0.0936-0.1641-0.05020.1224-0.0027-0.0921-0.03120.11350.05250.11730.0246-0.04410.19290.00330.08426.61570.7547.8612
192.5968-2.7439-0.20334.21281.74143.4754-0.10680.2106-0.1259-0.2459-0.1623-0.45780.09330.39490.09470.1920.09690.08240.21550.06380.20949.0854-10.754245.8075
201.4123-2.2651-1.0433.69671.36352.255-0.0330.1018-0.57040.02030.074-0.53530.42610.3844-0.0730.6350.22350.2790.44330.17230.565511.7727-20.782545.6198
210.1786-0.25350.46710.3559-0.66031.22490.20060.1002-0.114-0.1214-0.0637-0.36540.06140.2079-0.06690.31130.00910.08060.6227-0.29420.945218.4182-4.281955.3284
221.42852.91890.1469.56782.03261.1431-0.13290.2380.0373-0.1904-0.0355-0.684-0.05950.37360.10210.14-0.061-0.01250.3088-0.01160.246716.58668.080554.7941
231.6662-0.3203-2.45742.0029-1.26993.8421-0.18160.32070.1649-0.20860.034-0.1304-0.09760.13890.06880.49-0.4169-0.24070.28950.10510.301115.774421.138755.9075
240.747-0.2033-0.02731.16590.78030.5372-0.0090.26870.3297-0.2095-0.0047-0.0892-0.2634-0.01710.02070.68090.1575-0.8284-0.00330.37990.647412.037530.593458.5613
253.6477-0.2332-0.60238.462-1.19933.3535-0.01860.03270.2058-0.14410.02050.4184-0.2438-0.4651-0.02510.37580.2571-0.46570.1570.08470.3568.088723.999160.5633
260.82910.42090.15270.79970.70581.3235-0.0623-0.1665-0.09840.17280.0460.0396-0.03910.1785-0.01450.15480.0607-0.03540.1688-0.02720.12538.06438.833460.4183
273.92613.67020.18064.6241-1.64267.34650.034-0.1228-0.67850.14820.1098-0.08350.97120.2379-0.06420.32210.0123-0.03010.29050.12250.58669.8316-7.655158.7509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:10)
2X-RAY DIFFRACTION2(chain A and resid 11:20)
3X-RAY DIFFRACTION3(chain A and resid 21:25)
4X-RAY DIFFRACTION4(chain A and resid 26:33)
5X-RAY DIFFRACTION5(chain A and resid 34:43)
6X-RAY DIFFRACTION6(chain A and resid 44:61)
7X-RAY DIFFRACTION7(chain A and resid 62:68)
8X-RAY DIFFRACTION8(chain A and resid 69:76)
9X-RAY DIFFRACTION9(chain A and resid 77:89)
10X-RAY DIFFRACTION10(chain A and resid 90:98)
11X-RAY DIFFRACTION11(chain A and resid 99:116)
12X-RAY DIFFRACTION12(chain A and resid 117:126)
13X-RAY DIFFRACTION13(chain A and resid 127:137)
14X-RAY DIFFRACTION14(chain A and resid 138:154)
15X-RAY DIFFRACTION15(chain A and resid 155:162)
16X-RAY DIFFRACTION16(chain A and resid 163:185)
17X-RAY DIFFRACTION17(chain A and resid 186:196)
18X-RAY DIFFRACTION18(chain A and resid 197:207)
19X-RAY DIFFRACTION19(chain A and resid 208:213)
20X-RAY DIFFRACTION20(chain A and resid 214:220)
21X-RAY DIFFRACTION21(chain B and resid 23:28)
22X-RAY DIFFRACTION22(chain B and resid 29:39)
23X-RAY DIFFRACTION23(chain B and resid 40:46)
24X-RAY DIFFRACTION24(chain B and resid 47:54)
25X-RAY DIFFRACTION25(chain B and resid 55:60)
26X-RAY DIFFRACTION26(chain B and resid 61:74)
27X-RAY DIFFRACTION27(chain B and resid 75:83)

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