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- PDB-1m3x: Photosynthetic Reaction Center From Rhodobacter Sphaeroides -

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Basic information

Entry
Database: PDB / ID: 1m3x
TitlePhotosynthetic Reaction Center From Rhodobacter Sphaeroides
Components(Photosynthetic Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / alpha helix / membrane protein
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 / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / 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 Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / NONADEC-10-ENOIC ACID / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / SPHEROIDENE / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / NONADEC-10-ENOIC ACID / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / SPHEROIDENE / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Reaction center protein H chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCamara-Artigas, A. / Brune, D. / Allen, J.P.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Interactions between lipids and bacterial reaction centers determined by protein crystallography.
Authors: Camara-Artigas, A. / Brune, D. / Allen, J.P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Individual interactions influence the crystalline order for membrane proteins
Authors: Camara-Artigas, A. / Magee, C.L. / Williams, J.C. / Allen, J.P.
History
DepositionJul 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE FOLLOWING LIGANDS HAVE ATOMS MISSING DUE TO LACK OF ELECTRON DENSITY: BCL 850, U10 ...HETEROGEN THE FOLLOWING LIGANDS HAVE ATOMS MISSING DUE TO LACK OF ELECTRON DENSITY: BCL 850, U10 857, U10 858, CDL 900, PC2 901, GGD 902.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,83617
Polymers93,8113
Non-polymers11,02514
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34860 Å2
ΔGint-255 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.800, 141.800, 187.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Photosynthetic Reaction center protein ... , 3 types, 3 molecules LMH

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


Mass: 31346.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: Protein Photosynthetic Reaction center protein M chain / reaction center M subunit


Mass: 34398.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02953, UniProt: P0C0Y9*PLUS
#3: Protein Photosynthetic Reaction center protein H chain / reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P11846, UniProt: P0C0Y7*PLUS

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Non-polymers , 10 types, 217 molecules

#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#5: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#6: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#7: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#8: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H60O
#11: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#12: Chemical ChemComp-GGD / NONADEC-10-ENOIC ACID 2-[3,4-DIHYDROXY-6-HYDROXYMETHYL-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRAN-2-YLOXY] -1-OCTADEC-9-ENOYLOXYMETHYL-ETHYL ESTER / GLUCOSYL-GALACTOSYL DIACYL-GLYCEROL


Mass: 959.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C52H94O15
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: POTASIUM PHOSPHATE, LDAO, HEPTANE TRIOL, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.5 %heptano-1,2,3-triol1drop
20.1 %lauryl dimethylamine oxide1drop
32.0 %dioxane1drop
40.75 Mpotassium phosphate1droppH7.4
50.12 mMprotein1drop
61.6 Mpotassium phosphate1reservoirpH7.4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000
Details: 58 cm long, Pt-coated, fused silica, vertical focus mirror; Cyclindrically bent triangular Si(111) asymmetric cut
RadiationMonochromator: horizontal focus monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.55→30.83 Å / Num. obs: 68970 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.109 / Net I/σ(I): 4.3
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.5 / Num. unique all: 34173 / Rsym value: 0.364 / % possible all: 92.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 69691 / Num. measured all: 564825
Reflection shell
*PLUS
Lowest resolution: 2.65 Å / % possible obs: 92.5 %

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1QOV

1qov


Resolution: 2.55→29.91 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 6936 10.1 %RANDOM
Rwork0.185 ---
all-75734 --
obs-68531 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.9782 Å2 / ksol: 0.326599 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20.24 Å20 Å2
2--2.5 Å20 Å2
3----4.99 Å2
Refine analyzeLuzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.55→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6454 0 666 203 7323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 1076 10.2 %
Rwork0.24 9494 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMLIPIDOS.TOP
X-RAY DIFFRACTION3RC_ANA_WT.PARWATER.TOP
X-RAY DIFFRACTION4LIPIDOS.PARION.TOP
X-RAY DIFFRACTION5ION.PARRC_ANA_WT.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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