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- PDB-7q7n: Room temperature structure of the Rhodobacter Sphaeroides Photosy... -

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Basic information

Entry
Database: PDB / ID: 7q7n
TitleRoom temperature structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H mutant at 120 MPa helium gas pressure in a sapphire capillary
Components(Reaction center protein ...) 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 / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 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: 2.87 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
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37110 Å2
ΔGint-226 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.130, 102.130, 237.610
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 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 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 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, 166 molecules

#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-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


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


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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.39 Å3/Da / Density % sol: 63.71 %
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 environment: gaseous He / Ambient pressure: 120000 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
Diffraction measurementSpecimen support: sapphire capillary
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.477 Å / Relative weight: 1
ReflectionResolution: 2.87→46.91 Å / Num. obs: 28804 / % possible obs: 96.97 % / Redundancy: 6.6 % / Biso Wilson estimate: 45.83 Å2 / CC1/2: 0.935 / CC star: 0.983 / Rmerge(I) obs: 0.48 / Rpim(I) all: 0.186 / Rrim(I) all: 0.517 / Net I/σ(I): 3.39
Reflection shellResolution: 2.87→2.973 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.012 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2803 / CC1/2: 0.367 / CC star: 0.733 / Rpim(I) all: 0.771 / Rrim(I) all: 2.163 / % possible all: 96.07
Cell measurementPressure: 120000 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: 2.87→46.91 Å / SU ML: 0.3327 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1371 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2277 1157 4.02 %
Rwork0.1892 27613 -
obs0.1908 28770 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.62 Å2
Refinement stepCycle: LAST / Resolution: 2.87→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6461 0 674 142 7277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247511
X-RAY DIFFRACTIONf_angle_d0.546910276
X-RAY DIFFRACTIONf_chiral_restr0.03871018
X-RAY DIFFRACTIONf_plane_restr0.00331336
X-RAY DIFFRACTIONf_dihedral_angle_d11.76434204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-30.32581410.27923355X-RAY DIFFRACTION96.23
3-3.160.30121420.25433387X-RAY DIFFRACTION97.14
3.16-3.360.25371400.22823417X-RAY DIFFRACTION97.94
3.36-3.620.22431460.1943432X-RAY DIFFRACTION97.68
3.62-3.980.23181440.16413420X-RAY DIFFRACTION97.24
3.98-4.550.17741460.153471X-RAY DIFFRACTION97.68
4.55-5.740.17681490.16333514X-RAY DIFFRACTION97.58
5.74-46.910.25081490.1893617X-RAY DIFFRACTION94.77
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)
14.081893032010.1269320383386.107933325511.07330749826-0.3743232602499.35015444767-0.155847681747-0.460296060070.3066523502160.0644580766155-0.1377834445020.187085432508-0.351411677386-0.8251944143170.3489737684970.3174441330960.02181479632070.05364717176280.255828072291-0.01683497869890.418824060575-20.423384079648.6083904309-32.8750629504
21.185502987861.044533070790.8776129688371.716842489630.8808833707790.901644974343-0.133994498191-0.04600592330150.261360801165-0.143658643082-0.1204570320770.38597090578-0.292430839771-0.1442544127480.2719936135560.3289101602540.0280316467337-0.003449123749050.3363956104450.006389150470030.341053835254-25.436425025541.0103970168-55.0757288358
32.65238145662-0.1004743850741.395460242123.240227481960.3794269859140.9750886009770.01044949343640.436521102453-0.431199916991-0.2179837781590.297050983926-0.2769630457070.1212100034380.374334711895-0.2972845146380.3164293938160.0234625878885-0.002418887807140.416713635503-0.1304768649320.268515376201-13.209363971319.7353638074-61.9918836549
43.58443473669-4.40101917431-0.4941510562275.5021569987-0.05617501976466.71171191555-0.4524441733860.388465778264-0.432565450313-0.3098626271440.4046995008720.3273874645860.653404273884-0.4271075934920.01204514011580.2779310453390.00103210122283-0.07334865507940.354839445995-0.06304164335730.140441737705-25.929759720123.3225939731-58.9430785555
54.989619880761.12576268415-1.939014559125.10262193903-0.7107037303614.957374915830.02556654012710.0238263252326-0.03879875932220.4873603006990.1537660892740.61022253427-0.167391464855-0.514331039299-0.194175581390.1737213961730.03875103717860.01436542553450.2531897333080.005697512547320.292100428923-36.004471194733.6818184665-45.9659414969
61.50814196304-0.4103080319640.4784567861081.686966756550.336293994271.653043969470.098106243335-0.800430256229-0.1265968082760.41766383980.2105586598270.351720845323-0.0266675575626-1.0143433609-0.08083609118240.3210802434290.0002571851699880.1824403333010.566384330490.03996515046250.489856147063-39.953190696230.3822044795-20.7770532315
75.032024323741.288518776720.8977108245384.704034667780.7820018161133.722208612020.0733588087843-0.6723359448830.2376808668790.4035374010540.02614447981160.693932931719-0.396161246992-0.465021835492-0.1494235390150.556985135177-0.05571672107810.1164378284370.545296144698-0.006913375958050.25551412075-34.080485934326.2694730606-7.30892386435
81.33654917282-0.163773028988-0.4143366502621.30460656513-1.109493518274.82678750420.112989695929-0.0460392629011-0.04895590444760.146217992787-0.03904932618930.1196957080930.114834927684-0.478533364705-0.08989331181590.287915871891-0.0346690798270.0150062038020.2487726354650.03911190506610.318993246355-29.355052224222.9290785266-30.66091605
91.98020902770.439489727743-0.6252346182950.199133724513-0.1908903701841.617838523390.0492462921171-0.3195607412780.05314743365740.1810107663620.06160380179510.06759851698850.252371330501-0.160213641872-0.08861692818410.329271863393-0.02727567579550.0170880388930.2779123391820.03709447637260.245166877744-14.74678173623.1198263032-18.3338005757
100.9192744522170.5271263339130.1076295314081.85929362321-0.4592928963271.55057454421-0.08848909081740.182991177712-0.180454803258-0.2889692002830.113724071128-0.2520239652460.2403170645990.154110328576-0.02253160759450.1723163306380.02737741873640.01520061991920.282144612843-0.03175707525950.246866861102-4.1530429522728.4246326039-39.4585715019
114.276931198683.895392979430.9603666040574.4885703919-0.4340401557667.596171342330.222554291409-1.14163752048-1.66942013170.762272632295-0.319906349538-0.786483628413-0.3434309659541.112172982560.0904523349780.51716606543-0.0726655272612-0.1029397792350.5231853913150.2298264729040.608193515689-7.315512003158.64314953967-10.8044312121
122.756455627891.48799904826-0.3152946852012.8427338007-1.01284313415.267301730720.195646258866-0.465095563793-2.545799009861.29855026353-0.184338173247-0.1799771667811.18738907347-0.648950242639-0.02417786034820.591253591771-0.05825166317430.06410159892370.5266349933470.2304612213851.447085139039.122730101393.06681624083-8.11072017136
133.495814792355.05840065484-0.1093120377847.596764459980.9095375527873.667061589420.1090625310470.210685981018-0.302104291679-0.0586765620591-0.056281653317-0.2059823341580.24453502228-0.209588939339-0.06761245913680.2738809181610.111131310275-0.01571040413550.3245693017030.003880873071880.3084611622363.3123488399422.2698290755-47.9520308324
140.6355762439421.74437510148-2.332538879485.94881559761-7.460690897489.86611923949-0.298694208081-0.0740262825148-0.143560413634-0.2433378777870.0518479518041-0.2475841420120.368222303039-0.512569825670.2487686376550.317526497305-0.0756912285715-0.05365329434650.4468885857410.04340511943610.40443272338217.80001516323.6636883878-21.1282602469
152.40667712694-0.1936289585360.2122880817986.911971463731.685845199190.6187263814690.0764704329432-0.364647350863-0.3403283358060.780311270214-0.141345753391-0.754745093490.1239397616890.2140200159670.007968793311820.447909835796-0.0160576009874-0.1140358390960.5055794905410.1798155609160.41013591528214.719233365921.5618416317-8.38081862141
160.8337090009180.2378067129860.1928269705930.549234816854-0.1113085173740.8071871550510.0478382246303-0.0805048933689-0.03762561926150.0995601011197-0.055063490445-0.0923530920631-0.1023292360690.08428589746250.01641706647720.220278642259-0.03076413370060.01500961995040.216584321820.01846393593670.245468702688-4.3909766199835.0078883492-27.7373210923
177.582564808665.6263268139-7.894733926125.40651295908-6.689535644728.785975600270.586300091492-0.6457073436141.181341504431.002037807940.2401067806110.553691223702-0.493958233423-0.59948488701-0.7291980899150.626003338398-0.08506267059930.06582700328370.470888639548-0.04228301669470.282852104887-10.727276848741.7719543781-4.20007940681
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 280 )
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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