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- PDB-5b5n: Crystal structure of the Ba-substituted LH1-RC complex from Tch. ... -

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Basic information

Entry
Database: PDB / ID: 5b5n
TitleCrystal structure of the Ba-substituted LH1-RC complex from Tch. tepidum
Components
  • (Photosynthetic reaction center ...) x 4
  • LH1 alpha polypeptide
  • LH1 beta polypeptide
KeywordsPHOTOSYNTHESIS / Bacterial photosynthesis / Light-harvesting complex
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / photosynthesis / endomembrane system / electron transfer activity ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / photosynthesis / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Multiheme cytochrome c family profile. / Light-harvesting complex / 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 / Multiheme cytochrome 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 / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGW / PHOSPHATE ION ...: / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGW / PHOSPHATE ION / Ubiquinone-8 / Reaction center protein M chain / LH1 beta polypeptide / LH1 alpha polypeptide / Reaction center protein L chain / Photosynthetic reaction center cytochrome c subunit / Photosynthetic reaction center H subunit
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWang-Otomo, Z.-Y. / Yu, L.-J.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis for the Unusual Qy Red-Shift and Enhanced Thermostability of the LH1 Complex from Thermochromatium tepidum.
Authors: Yu, L.J. / Kawakami, T. / Kimura, Y. / Wang-Otomo, Z.Y.
History
DepositionMay 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: 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 / pdbx_initial_refinement_model / refine_hist / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
L: Photosynthetic reaction center L subunit
M: Photosynthetic reaction center M subunit
H: Photosynthetic reaction center H subunit
A: LH1 alpha polypeptide
B: LH1 beta polypeptide
D: LH1 alpha polypeptide
E: LH1 beta polypeptide
F: LH1 alpha polypeptide
G: LH1 beta polypeptide
I: LH1 alpha polypeptide
J: LH1 beta polypeptide
K: LH1 alpha polypeptide
N: LH1 beta polypeptide
O: LH1 alpha polypeptide
P: LH1 beta polypeptide
Q: LH1 alpha polypeptide
R: LH1 beta polypeptide
S: LH1 alpha polypeptide
T: LH1 beta polypeptide
U: LH1 alpha polypeptide
V: LH1 beta polypeptide
W: LH1 alpha polypeptide
X: LH1 beta polypeptide
Y: LH1 alpha polypeptide
Z: LH1 beta polypeptide
1: LH1 alpha polypeptide
2: LH1 beta polypeptide
3: LH1 alpha polypeptide
4: LH1 beta polypeptide
5: LH1 alpha polypeptide
6: LH1 beta polypeptide
7: LH1 alpha polypeptide
8: LH1 beta polypeptide
9: LH1 alpha polypeptide
0: LH1 beta polypeptide
o: Photosynthetic reaction center cytochrome c subunit
x: Photosynthetic reaction center L subunit
y: Photosynthetic reaction center M subunit
t: Photosynthetic reaction center H subunit
m: LH1 alpha polypeptide
n: LH1 beta polypeptide
p: LH1 alpha polypeptide
q: LH1 beta polypeptide
r: LH1 alpha polypeptide
s: LH1 beta polypeptide
u: LH1 alpha polypeptide
v: LH1 beta polypeptide
w: LH1 alpha polypeptide
z: LH1 beta polypeptide
AA: LH1 alpha polypeptide
AB: LH1 beta polypeptide
AC: LH1 alpha polypeptide
AD: LH1 beta polypeptide
AE: LH1 alpha polypeptide
AF: LH1 beta polypeptide
AG: LH1 alpha polypeptide
AH: LH1 beta polypeptide
AI: LH1 alpha polypeptide
AJ: LH1 beta polypeptide
AK: LH1 alpha polypeptide
AL: LH1 beta polypeptide
d: LH1 alpha polypeptide
e: LH1 beta polypeptide
f: LH1 alpha polypeptide
g: LH1 beta polypeptide
h: LH1 alpha polypeptide
i: LH1 beta polypeptide
j: LH1 alpha polypeptide
k: LH1 beta polypeptide
l: LH1 alpha polypeptide
c: LH1 beta polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)782,466256
Polymers666,88672
Non-polymers115,580184
Water1086
1
C: Photosynthetic reaction center cytochrome c subunit
L: Photosynthetic reaction center L subunit
M: Photosynthetic reaction center M subunit
H: Photosynthetic reaction center H subunit
A: LH1 alpha polypeptide
B: LH1 beta polypeptide
D: LH1 alpha polypeptide
E: LH1 beta polypeptide
F: LH1 alpha polypeptide
G: LH1 beta polypeptide
I: LH1 alpha polypeptide
J: LH1 beta polypeptide
K: LH1 alpha polypeptide
N: LH1 beta polypeptide
O: LH1 alpha polypeptide
P: LH1 beta polypeptide
Q: LH1 alpha polypeptide
R: LH1 beta polypeptide
S: LH1 alpha polypeptide
T: LH1 beta polypeptide
U: LH1 alpha polypeptide
V: LH1 beta polypeptide
W: LH1 alpha polypeptide
X: LH1 beta polypeptide
Y: LH1 alpha polypeptide
Z: LH1 beta polypeptide
1: LH1 alpha polypeptide
2: LH1 beta polypeptide
3: LH1 alpha polypeptide
4: LH1 beta polypeptide
5: LH1 alpha polypeptide
6: LH1 beta polypeptide
7: LH1 alpha polypeptide
8: LH1 beta polypeptide
9: LH1 alpha polypeptide
0: LH1 beta polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,233128
Polymers333,44336
Non-polymers57,79092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area212280 Å2
ΔGint-1818 kcal/mol
Surface area101490 Å2
MethodPISA
2
o: Photosynthetic reaction center cytochrome c subunit
x: Photosynthetic reaction center L subunit
y: Photosynthetic reaction center M subunit
t: Photosynthetic reaction center H subunit
m: LH1 alpha polypeptide
n: LH1 beta polypeptide
p: LH1 alpha polypeptide
q: LH1 beta polypeptide
r: LH1 alpha polypeptide
s: LH1 beta polypeptide
u: LH1 alpha polypeptide
v: LH1 beta polypeptide
w: LH1 alpha polypeptide
z: LH1 beta polypeptide
AA: LH1 alpha polypeptide
AB: LH1 beta polypeptide
AC: LH1 alpha polypeptide
AD: LH1 beta polypeptide
AE: LH1 alpha polypeptide
AF: LH1 beta polypeptide
AG: LH1 alpha polypeptide
AH: LH1 beta polypeptide
AI: LH1 alpha polypeptide
AJ: LH1 beta polypeptide
AK: LH1 alpha polypeptide
AL: LH1 beta polypeptide
d: LH1 alpha polypeptide
e: LH1 beta polypeptide
f: LH1 alpha polypeptide
g: LH1 beta polypeptide
h: LH1 alpha polypeptide
i: LH1 beta polypeptide
j: LH1 alpha polypeptide
k: LH1 beta polypeptide
l: LH1 alpha polypeptide
c: LH1 beta polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,233128
Polymers333,44336
Non-polymers57,79092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area213360 Å2
ΔGint-1827 kcal/mol
Surface area100560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.830, 148.560, 210.000
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Photosynthetic reaction center ... , 4 types, 8 molecules CoLxMyHt

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 36630.484 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-333 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P5
#2: Protein Photosynthetic reaction center L subunit


Mass: 31520.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P3
#3: Protein Photosynthetic reaction center M subunit


Mass: 35975.992 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-319 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: A8ASG6
#4: Protein Photosynthetic reaction center H subunit


Mass: 28213.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P9

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Protein / Protein/peptide , 2 types, 64 molecules ADFIKOQSUWY13579mpruwAAACAEAGAIAKdfh...

#5: Protein ...
LH1 alpha polypeptide


Mass: 7034.442 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P2
#6: Protein/peptide ...
LH1 beta polypeptide


Mass: 5534.452 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P1

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Non-polymers , 12 types, 190 molecules

#7: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical...
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Ba
#9: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#10: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H76N4O6
#11: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H74O4
#12: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#13: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#14: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H72O2
#15: Chemical...
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C42H60O2
#16: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#17: Chemical ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3000, barium chloride, decylphosphocholine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→49.9 Å / Num. obs: 133051 / % possible obs: 93 % / Redundancy: 22.8 % / Net I/σ(I): 8.6
Reflection shellResolution: 3.3→3.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMM

3wmm


Resolution: 3.3→49.9 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3133 6652 5 %
Rwork0.2793 --
obs0.281 133050 92.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44418 0 7457 6 51881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03253919
X-RAY DIFFRACTIONf_angle_d2.15874475
X-RAY DIFFRACTIONf_dihedral_angle_d18.01318873
X-RAY DIFFRACTIONf_chiral_restr0.1567670
X-RAY DIFFRACTIONf_plane_restr0.0118810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.33750.38892130.39454055X-RAY DIFFRACTION90
3.3375-3.37680.41022160.38514105X-RAY DIFFRACTION91
3.3768-3.4180.38972130.36914045X-RAY DIFFRACTION89
3.418-3.46120.38242100.36913982X-RAY DIFFRACTION87
3.4612-3.50670.3692090.35223971X-RAY DIFFRACTION88
3.5067-3.55480.35452180.35094146X-RAY DIFFRACTION91
3.5548-3.60550.36212140.34594060X-RAY DIFFRACTION90
3.6055-3.65930.39732110.32453999X-RAY DIFFRACTION88
3.6593-3.71650.32812130.32064044X-RAY DIFFRACTION88
3.7165-3.77740.31532140.30254061X-RAY DIFFRACTION91
3.7774-3.84250.32542170.30274127X-RAY DIFFRACTION91
3.8425-3.91240.30372120.29574036X-RAY DIFFRACTION89
3.9124-3.98760.30572120.28954010X-RAY DIFFRACTION88
3.9876-4.0690.28772130.26914064X-RAY DIFFRACTION90
4.069-4.15740.27322170.274118X-RAY DIFFRACTION91
4.1574-4.2540.30992180.26674149X-RAY DIFFRACTION91
4.254-4.36040.3162210.27134198X-RAY DIFFRACTION92
4.3604-4.47820.32732180.27984140X-RAY DIFFRACTION91
4.4782-4.60990.29642220.26514221X-RAY DIFFRACTION92
4.6099-4.75860.29092270.25364305X-RAY DIFFRACTION95
4.7586-4.92850.29742240.25374264X-RAY DIFFRACTION93
4.9285-5.12560.30992290.24794374X-RAY DIFFRACTION95
5.1256-5.35870.27842260.2424300X-RAY DIFFRACTION95
5.3587-5.64080.29012330.25054411X-RAY DIFFRACTION97
5.6408-5.99370.30912360.2544491X-RAY DIFFRACTION98
5.9937-6.45560.27492360.25714490X-RAY DIFFRACTION98
6.4556-7.10360.31222400.25954553X-RAY DIFFRACTION99
7.1036-8.12760.30282390.25584546X-RAY DIFFRACTION99
8.1276-10.22550.27322420.24314599X-RAY DIFFRACTION100
10.2255-49.90660.34262390.30584534X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 24.59 Å / Origin y: -15.8433 Å / Origin z: 49.1244 Å
111213212223313233
T0.6759 Å2-0.0594 Å2-0.2451 Å2-0.6048 Å20.0151 Å2--1.1633 Å2
L1.087 °20.0064 °2-1.8979 °2-0.3497 °20.1216 °2--5.0174 °2
S-0.0028 Å °-0.1278 Å °-0.0638 Å °0.0071 Å °-0.0614 Å °-0.01 Å °-0.0285 Å °0.1376 Å °-0.0051 Å °
Refinement TLS groupSelection details: all

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