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- PDB-7q7f: Room temperature structure of the Rhodobacter Sphaeroides Photosy... -

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Basic information

Entry
Database: PDB / ID: 7q7f
TitleRoom temperature structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H mutant at atmospheric pressure
Components(Reaction center protein ...Photosynthetic reaction centre) x 3
KeywordsELECTRON TRANSPORT / HPMX / high-pressure macromolecular crystallography / sapphire capillary / room temperature
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / metal ion binding
Similarity search - Function
Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily ...Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CITRIC ACID / : / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-7 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLieske, J. / Guenther, S. / Saouane, S. / Selikhanov, G.K. / Gabdulkhakov, A.G. / Meents, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B0405A Germany
Citation
Journal: To Be Published
Title: Fixed-target high-pressure macromolecular crystallography
Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / ...Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / Gabdulkhakov, A.G. / Selikhanov, G.K. / Chapman, H.N. / Meents, A.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,33727
Polymers91,4073
Non-polymers9,92924
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36910 Å2
ΔGint-224 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.500, 102.500, 237.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

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Reaction center protein ... , 3 types, 3 molecules HLM

#1: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 26170.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: puhA / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 31360.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: pufL / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y8
#3: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 33876.895 Da / Num. of mol.: 1 / Mutation: F197H, S8T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: pufM / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y9

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Non-polymers , 11 types, 178 molecules

#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C14H31NO / Feature type: SUBJECT OF INVESTIGATION / Comment: LDAO, detergent*YM
#5: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-UQ7 / UBIQUINONE-7


Mass: 658.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H66O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#13: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 20-25 mg/ml protein solution was mixed 1:1 with lipid sponge phase. The mixture was filled into a sealed plastic tip covered with an excess amount of 1 M trisodium citrate and incubated in ...Details: 20-25 mg/ml protein solution was mixed 1:1 with lipid sponge phase. The mixture was filled into a sealed plastic tip covered with an excess amount of 1 M trisodium citrate and incubated in the dark at 289 K for 1 week.
Pressure: 101.325 kPa

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Data collection

DiffractionAmbient pressure: 101.325 kPa / Mean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.477 Å
DetectorType: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Oct 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.477 Å / Relative weight: 1
ReflectionResolution: 2.75→47.07 Å / Num. obs: 33826 / % possible obs: 99.77 % / Redundancy: 10.7 % / Biso Wilson estimate: 49.57 Å2 / CC1/2: 0.976 / CC star: 0.994 / Rmerge(I) obs: 0.414 / Rpim(I) all: 0.128 / Rrim(I) all: 0.435 / Net I/σ(I): 5.13
Reflection shellResolution: 2.75→2.848 Å / Redundancy: 9.9 % / Rmerge(I) obs: 2.351 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 3326 / CC1/2: 0.355 / CC star: 0.724 / Rpim(I) all: 0.751 / Rrim(I) all: 2.475 / % possible all: 99.61
Cell measurementPressure: 101.325 kPa

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.13-2998_9999refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3Y

3v3y


Resolution: 2.75→47.07 Å / SU ML: 0.3284 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1931 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2244 1358 4.02 %
Rwork0.1791 32453 -
obs0.1809 33811 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.02 Å2
Refinement stepCycle: LAST / Resolution: 2.75→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 674 154 7294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00257496
X-RAY DIFFRACTIONf_angle_d0.554610265
X-RAY DIFFRACTIONf_chiral_restr0.03891018
X-RAY DIFFRACTIONf_plane_restr0.00361337
X-RAY DIFFRACTIONf_dihedral_angle_d12.21544190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.850.31951340.28283186X-RAY DIFFRACTION99.61
2.85-2.960.2991320.2643157X-RAY DIFFRACTION99.88
2.96-3.10.28891370.23923201X-RAY DIFFRACTION99.97
3.1-3.260.24551310.21233173X-RAY DIFFRACTION99.97
3.26-3.460.22091360.18313225X-RAY DIFFRACTION99.94
3.46-3.730.21611330.16653214X-RAY DIFFRACTION100
3.73-4.110.20521370.13893258X-RAY DIFFRACTION100
4.11-4.70.17041360.13763257X-RAY DIFFRACTION99.91
4.7-5.920.17761390.15593297X-RAY DIFFRACTION99.74
5.92-47.070.26411430.18753485X-RAY DIFFRACTION99.1
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)
13.532000290450.4262320814115.349317850912.352467691430.2683643633229.09279098285-0.0234415849141-0.4514732588670.2823261759710.170072597162-0.1348545195860.173006227172-0.335746922965-0.7513076494590.2085014941660.3602954125-0.02984862332170.06821638960890.325757355159-0.008921594666280.43408347915-20.459417996748.8196675357-32.8798966472
22.015054778640.8471023699030.9330778113071.788621975190.08944048502970.5259490055190.03103772041430.04286205754620.3634457764270.0138352048721-0.1160317205270.32497758751-0.0707733839232-0.1093044780690.1017331780560.332695405683-0.0288609396697-0.009303856348120.3890043446810.01224952787690.418646376546-25.499321129841.1413608587-55.1468020799
33.406560749680.1936027773441.520749136113.39528251270.8184199250411.44910232740.06804739077960.514881469013-0.54037550644-0.1347906870020.304275942383-0.432568640420.162912916380.375802015409-0.3499470082630.3325636878490.0172005620132-0.02003541738590.502696421948-0.1475415529480.384271485982-13.246684275319.805603952-62.2824348152
43.87694555357-3.866602807970.09562537310255.81998627591-0.1836119473977.38052821426-0.02989980914260.430477417625-0.588015715654-0.1887098076640.06191350465340.6097837020290.750748917573-0.474660591468-0.05220302897240.270224424287-0.0442608003139-0.05942347563050.419207145288-0.06110862792110.323435249612-25.993894487323.4103630128-59.008796084
54.481424017160.893866262282-1.423880600094.84587814148-0.1250556436233.438334667590.202576445381-0.1430496899760.3096003978930.3049671623220.04745302875390.940885995229-0.127137730736-0.436654554336-0.2650722124510.2545932188270.03093297014380.04935067307950.322789228890.02054120921070.442331282293-36.137472400333.8059318432-46.0317111709
62.723649504550.02128703537161.582258468362.058094044390.3649410297584.47345979780.0653648935533-1.00056534537-0.08372277527060.626064996206-0.1973978505410.3565472174630.0617744885447-1.089828430950.1344255817070.470020135683-0.08084492961330.2021513032470.6436820875920.001648013280960.512054001342-40.112218833930.485063721-20.824832284
73.844971868790.5422162359740.6093785200645.99441034414-0.09352157034652.664524114260.170273025354-0.5183882928560.1330135199070.675719526341-0.3048545114680.427232020278-0.133158318191-0.8768691364790.09634590896830.656965531426-0.1579550305910.08551751334450.7910843792770.02864188478020.388896552874-34.16271920126.3535342224-7.28107874834
81.2175439796-0.00924777288586-0.5517765213091.06024802178-0.7682336982523.124835361840.193780559222-0.15200387771-0.1760679504290.24304397732-0.1186723802580.1148196770550.0658841973603-0.272375375727-0.04946790723910.339308745127-0.1151230353840.02224943851290.3259695567650.03120830382820.404428164632-29.45277478322.9852018819-30.6864554523
91.733363117441.07989663259-1.046954878111.19791973238-0.3554853006431.678111082670.171475321854-0.442262631199-0.1629785797710.376846597458-0.173116792477-0.0379956057890.235394646894-0.1925351689260.008004365053920.397969863468-0.113797590108-0.03882279889650.4114514187780.06327627032910.333775328801-14.798976815823.1888183831-18.3323507137
100.930017500431-0.05686837415260.01156747106110.2503703201710.3626131126890.8190337110960.04553118031570.0291019938483-0.1583913087450.00880198770264-0.0608215311698-0.09426508057260.03676180097720.09515926450180.02740779816610.259034170425-0.0135320506525-0.01463984759650.274381676948-0.02694931831520.285204030693-4.1643773711128.5151803318-39.4700959033
118.031425206851.523705368330.5371907529882.46337598992-0.46569412343.509773417240.111466603988-0.706018429682-1.480903192090.643906630862-0.124861924102-0.739127849418-0.4126322621060.860015720270.007951821922420.752135802073-0.23783831176-0.1777167843160.6624383767110.2193110384920.819893824285-7.360890011088.63075833613-10.7632738708
129.85264431199-5.46448101346-0.648411344316.16651362608-3.001925842757.410079391010.715171854403-1.16738577016-3.146939658010.992263799684-0.5122511539210.156792846010.621692967579-0.148063303455-0.1267922181190.733847515452-0.128134310684-0.2392651432560.8326575561960.3403679629941.431414004559.222240088983.44011693246-7.74433998767
132.904969784274.20806208488-0.1522236673996.484612149050.8925484229543.145892357130.2981277142250.324153649667-0.3779156215730.121608129423-0.124541669394-0.2519520870460.268939551924-0.0783714778063-0.1848158315030.3448490037140.113016624828-0.06568988171610.3982909628320.0221961968240.4556526118093.3158368745322.3200740851-47.9506238958
140.7550329540911.4276457707-1.798377535673.20190421657-3.714722963564.803587667-0.160984321783-0.180362366781-0.200379559128-0.0425262460265-0.00590399202541-0.2158226912790.319934581705-0.1466879902920.1398047529540.436209430706-0.0186877647109-0.1678834165310.5647231149040.0969062250470.62839902755317.850466641523.740327875-21.1555339646
153.53501382084-0.3820509418840.001412696682777.521228661761.604727830092.326245674140.0347231106698-0.478780507123-0.4885308959360.933151748808-0.0440648033493-0.8733580114890.05871892548320.459428088646-0.007622991069790.544187979809-0.081846767166-0.1962691455860.5788425414830.1843333073390.53649614464514.760648404421.630850207-8.32864091727
161.125988122660.1111945236840.1683157430150.60645166129-0.03437540230450.8387980947760.119659782014-0.194677159476-0.06203696622720.202987439727-0.125199534221-0.124851882464-0.08155430510410.1055828504010.00276886653840.307615165469-0.0947832285803-0.01881471898990.2846443492950.02357354078230.310498450956-4.4116560936335.1196775573-27.7375146849
174.237709829533.92530229551-3.8436061987.2298625379-1.610569968177.009624764550.211126134576-0.6551464822320.6810277949970.496364148972-0.0381222361220.547072143873-0.0897178720724-0.509754077412-0.1512197866280.66218938529-0.19672830.09453332069940.4780231844070.00283959876550.322549275016-10.72882838241.8869694051-4.15709038179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 10 through 56 )
2X-RAY DIFFRACTION2chain 'H' and (resid 57 through 112 )
3X-RAY DIFFRACTION3chain 'H' and (resid 113 through 226 )
4X-RAY DIFFRACTION4chain 'H' and (resid 227 through 249 )
5X-RAY DIFFRACTION5chain 'L' and (resid 1 through 31 )
6X-RAY DIFFRACTION6chain 'L' and (resid 32 through 56 )
7X-RAY DIFFRACTION7chain 'L' and (resid 57 through 83 )
8X-RAY DIFFRACTION8chain 'L' and (resid 84 through 132 )
9X-RAY DIFFRACTION9chain 'L' and (resid 133 through 198 )
10X-RAY DIFFRACTION10chain 'L' and (resid 199 through 249 )
11X-RAY DIFFRACTION11chain 'L' and (resid 250 through 267 )
12X-RAY DIFFRACTION12chain 'L' and (resid 268 through 281 )
13X-RAY DIFFRACTION13chain 'M' and (resid 2 through 53 )
14X-RAY DIFFRACTION14chain 'M' and (resid 54 through 77 )
15X-RAY DIFFRACTION15chain 'M' and (resid 78 through 112 )
16X-RAY DIFFRACTION16chain 'M' and (resid 113 through 285 )
17X-RAY DIFFRACTION17chain 'M' and (resid 286 through 301 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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