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- PDB-3d38: Crystal structure of new trigonal form of photosynthetic reaction... -

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Basic information

Entry
Database: PDB / ID: 3d38
TitleCrystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.
Components
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsPHOTOSYNTHESIS / detergent extraction / reaction center / microfludics / plugs / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / Electron transport / Heme / Iron / Lipoprotein / Membrane / Metal-binding / Transport / Bacteriochlorophyll / Chlorophyll / Chromophore / Formylation / Transmembrane / Magnesium
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 / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 / Multiheme cytochrome c family profile. / 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 / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / UBIQUINONE-1 / Reaction center protein H chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / UBIQUINONE-1 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsLi, L. / Nachtergaele, S.H.M. / Seddon, A.M. / Tereshko, V. / Ponomarenko, N. / Ismagilov, R.F. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Simple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device.
Authors: Li, L. / Nachtergaele, S. / Seddon, A.M. / Tereshko, V. / Ponomarenko, N. / Ismagilov, R.F.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_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_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

Downloads & links

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
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)144,98241
Polymers132,4104
Non-polymers12,57237
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25690 Å2
ΔGint-145.3 kcal/mol
Surface area47570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)241.171, 241.171, 113.391
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Photosynthetic reaction center cytochrome c subunit / Cytochrome c558/c559


Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P07173

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

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


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06008
#3: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009
#4: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010

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Non-polymers , 11 types, 196 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#7: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O3
#8: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#9: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B / Bacteriochlorophyll


Mass: 909.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O6
#10: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B / Pheophytin


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#11: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18O4
#12: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#13: Chemical ChemComp-MQ9 / MENAQUINONE-9 / Vitamin K2


Mass: 785.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H80O2
#14: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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

CrystalDensity Matthews: 7.19 Å3/Da / Density % sol: 82.9 %
Crystal growTemperature: 296 K / Method: plug-based microfluidics / pH: 6
Details: 9 mg/mL Protein, 4.6 mM LDAO, 10 mM Methyl-beta-cyclodextrin, 1.6-1.7 M Sulfate, 4.5% w/v Triethylammonium phosphate pH 6.0, 3% 1,2,3-heptanetriol, 30 mM NaH2PO4-Na2HPO4 pH 6.0, Plug-based ...Details: 9 mg/mL Protein, 4.6 mM LDAO, 10 mM Methyl-beta-cyclodextrin, 1.6-1.7 M Sulfate, 4.5% w/v Triethylammonium phosphate pH 6.0, 3% 1,2,3-heptanetriol, 30 mM NaH2PO4-Na2HPO4 pH 6.0, Plug-based Microfluidics, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 62037 / Num. obs: 62037 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 30.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0073refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2I5N
Resolution: 3.21→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.871 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3145 5.1 %RANDOM
Rwork0.192 ---
obs0.194 62025 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.435 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å21.94 Å20 Å2
2--3.88 Å20 Å2
3----5.82 Å2
Refinement stepCycle: LAST / Resolution: 3.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9282 0 870 159 10311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210503
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.99914441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63451173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64222.416418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.749151395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2651564
X-RAY DIFFRACTIONr_chiral_restr0.0850.21447
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218070
X-RAY DIFFRACTIONr_mcbond_it0.5521.55857
X-RAY DIFFRACTIONr_mcangle_it1.07329417
X-RAY DIFFRACTIONr_scbond_it1.30234646
X-RAY DIFFRACTIONr_scangle_it2.2754.55024
LS refinement shellResolution: 3.21→3.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 219 -
Rwork0.288 4131 -
all-4350 -
obs--95.92 %

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