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- PDB-7q7o: Room temperature structure of the Rhodobacter Sphaeroides Photosy... -

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Basic information

Entry
Database: PDB / ID: 7q7o
TitleRoom temperature structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H mutant at atmospheric pressure after high helium gas pressure release
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 / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily ...Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
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: 2.65 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
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36940 Å2
ΔGint-227 kcal/mol
Surface area29000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.520, 102.520, 237.680
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, 176 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 / Feature type: SUBJECT OF INVESTIGATION
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#13: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 63.99 %
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: 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
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: 2.65→47.07 Å / Num. obs: 37727 / % possible obs: 99.86 % / Redundancy: 17.1 % / Biso Wilson estimate: 46.12 Å2 / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.475 / Rpim(I) all: 0.115 / Rrim(I) all: 0.49 / Net I/σ(I): 6
Reflection shellResolution: 2.65→2.745 Å / Redundancy: 15.5 % / Rmerge(I) obs: 3.133 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 3691 / CC1/2: 0.329 / CC star: 0.703 / Rpim(I) all: 0.797 / Rrim(I) all: 3.238 / % possible all: 99.95
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: 2.65→47.07 Å / SU ML: 0.3293 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5838 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2148 1515 4.02 %
Rwork0.176 36198 -
obs0.1776 37713 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.51 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 674 152 7292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00337479
X-RAY DIFFRACTIONf_angle_d0.563510240
X-RAY DIFFRACTIONf_chiral_restr0.03841016
X-RAY DIFFRACTIONf_plane_restr0.00361333
X-RAY DIFFRACTIONf_dihedral_angle_d11.96164177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.740.32451360.29553228X-RAY DIFFRACTION99.94
2.74-2.830.31841330.273224X-RAY DIFFRACTION100
2.83-2.950.26671350.24263253X-RAY DIFFRACTION100
2.95-3.080.26481380.21753224X-RAY DIFFRACTION99.94
3.08-3.240.23051330.1963238X-RAY DIFFRACTION99.85
3.24-3.450.19511370.16993262X-RAY DIFFRACTION99.97
3.45-3.710.16881340.1513279X-RAY DIFFRACTION99.85
3.71-4.090.18751400.1343267X-RAY DIFFRACTION99.88
4.09-4.680.15921390.13243330X-RAY DIFFRACTION100
4.68-5.890.17531410.15313347X-RAY DIFFRACTION99.97
5.89-47.070.27181490.18943546X-RAY DIFFRACTION99.54
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)
13.901013107920.2835232141275.417110652382.1591253559-0.9671086984658.72184402423-0.0917911367365-0.4882573395710.3239454387260.0975211287805-0.1295494649510.155128335798-0.406687197187-0.727290022470.2553068759130.324079763190.006157350496520.07727664763830.28685301743-0.02508736457490.414835784298-20.465890386648.8614611674-32.9907655821
22.119499083341.381745691491.043429765542.334922710590.4723215785220.663512171644-0.03982864055410.1367867495120.361154577288-0.00618191734424-0.09155373906490.440030015211-0.155037198534-0.08956094052590.1340232536490.32842371764-0.00770424609387-0.01799939200020.3986728132070.02572600664640.420582105032-25.504796360641.1638421012-55.1282449155
33.327826997440.4682437067371.025107096453.414834393740.6684557196971.301216595040.008635641723470.606286357191-0.537740710918-0.08771236691160.322529150021-0.43349697710.1410938335380.369468601135-0.3190689558480.3153231245540.024474560236-0.02182475817230.504579858199-0.1428793314380.334210756098-13.218475888419.8613303237-62.1543574106
44.37416413017-3.700159611930.2217183864065.86601107689-0.8594218313228.42852367668-0.1423688722710.320851901749-0.688520029823-0.1754868690130.09066255763150.6359495820730.689539587257-0.546524028119-0.003313607249540.307740677322-0.0464147422575-0.05707902727580.326337296589-0.08200076414340.356593521613-26.022500292323.3854817582-59.0170268791
55.589840497810.423201251791-2.371249300553.96807618256-0.5083067013615.07309893780.166962303167-0.03101719381640.05732683064750.440799856920.007920537465520.631562513647-0.186943835222-0.475690810648-0.1932251754060.2437494187310.003526072462260.0349528040990.2775581452110.0007919436723810.392417680447-36.157377643433.8241009975-46.0203420292
63.26921249833-0.3000633525021.212581505342.168181966240.7389282954379.19617191423-0.0768016681903-0.849332989925-0.3051160789980.551837410878-0.2116256236310.385482363384-0.0799080490508-1.111863679370.3066964317730.475489364416-0.06280016451360.1897203123550.5565119930220.03578059266290.543174677918-40.101357581530.4972539478-20.7765810994
72.558576041670.4680633626591.407251894565.565279902230.667829546530.8784517863170.103194392199-0.5435941644970.2025415083830.444028301037-0.1684527360650.4306628433540.00395478658326-0.6628962964020.02184983546180.699685767053-0.2059837295060.1081068425940.7739774678550.05524377581160.413036510947-34.17475291126.3533312784-7.26417041186
81.973678522090.262275713148-0.9752457536611.17814131432-1.96778683624.724139955090.20248907293-0.14857135754-0.1096037282830.178537985689-0.05634654394180.1389768082590.196702384299-0.335307337636-0.1200288503310.366134424969-0.1026810826090.005275220918710.2785929059720.004605721580070.358862172031-29.463663656522.9961886646-30.679193125
91.552439587790.792319345352-0.4676424323291.09746526914-0.4857815424861.781903711530.185080024466-0.352009414077-0.07010356411020.331400403658-0.0765164848204-7.83666002591E-50.166242680665-0.213697923171-0.1043189596580.389963145591-0.107568511738-0.03172646682240.3535673651540.04319692880870.313263834957-14.80107992923.2059713912-18.3250137876
100.950114213958-0.3606148022910.2048792665180.3294973746790.2181492342490.9586365390270.04121405774890.00336832344921-0.13003093804-0.0437041075835-0.0779537391196-0.1651609364780.1272258951330.18649493010.01442224890560.270015046304-0.0291826432856-0.02555677073760.299864719648-0.03150742495670.283095146341-4.1598858331628.5158822663-39.4467182002
112.655941204752.44462341283-1.011383182292.68174976856-1.935145572875.703271333810.276924817519-1.47871126379-1.806195877410.64919349544-0.313501837263-0.807668295367-0.2717810861880.6333352673620.06513496591310.6303707474-0.230187930503-0.149937886020.6949389073430.2655683950160.804649276379-7.369413367828.64846615985-10.7640441335
127.34716830381-2.53375115057-0.2092560111937.77773101629-1.956108125058.547445896320.660975540996-0.871847833667-2.797495179341.3703943132-0.478738961715-0.1118047294521.49099813462-0.187116709753-0.1895613465120.772472094727-0.107754240224-0.242186246850.6812120120210.2541207785711.399902356569.244680693333.4273123207-7.71962354377
133.070566484184.51567645677-0.7695871361066.92388546637-0.1472439576773.57926976760.1441490895090.272209897575-0.414236116062-0.0565514002608-0.0771737773274-0.2116753878220.292689551177-0.0540832484667-0.09548395459450.3293287032120.0816246068047-0.07701527067870.3385125030480.00128384308410.4619427422613.3183643522622.3387596155-47.9276831764
140.3160290886641.41801026719-1.575063578769.47410125163-8.963980246639.10007546272-0.24651587486-0.106405542815-0.1485181920750.03966842646-0.21988466865-0.72661657730.3697731764830.01288286981480.4305354732310.38737121372-0.0742691852988-0.1418919219840.4595004066390.1410813396370.55993468645817.851899185523.777219225-21.129913595
153.97880703608-0.835184368561-0.5494160366048.816537827851.612221279642.605186489140.147820401759-0.504709149986-0.4437713778160.900528104747-0.148230752508-0.8481962848960.09450465913270.361030631177-0.01625246420610.584227509342-0.106640213949-0.213650490330.5358022017670.1959082522860.52168241416614.771209887421.6169867045-8.33964195244
160.9556960720740.1012894045190.547738531140.617187758041-0.1752872351271.185717025310.147373997454-0.161165102456-0.07549156913410.20626393975-0.125251908961-0.0800881026942-0.0282935771080.093513853495-0.02454679022110.311863633297-0.09014993603630.003723497582730.2991647982510.01363652504080.311125495868-4.4112059500935.1279859804-27.7279733843
175.104362808145.49078920218-5.552149690889.47387820334-4.996926016156.755979351830.280530836744-0.2253520280220.6915224180750.2149965652460.2097757739330.331186037136-0.268289700518-0.515075185789-0.4523220988930.751558521814-0.2562521440120.04913905395820.531925632904-0.04272573106070.299118614992-10.733216557441.8427939996-4.17143370371
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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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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