- PDB-1rg5: Structure of the photosynthetic reaction centre from Rhodobacter ... -
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Basic information
Entry
Database: PDB / ID: 1rg5
Title
Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1
Components
(Reaction center protein ...Photosynthetic reaction centre) x 3
Keywords
PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / CAROTENOIDLESS MUTANT / CAROTENOID BINDING SITE / 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 / : / HEPTANE-1,2,3-TRIOL / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / HEPTANE-1,2,3-TRIOL / 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
Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein
ReactioncenterproteinLchain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit
Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid. Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: Protein
ReactioncenterproteinMchain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit
Mass: 34398.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P02953, UniProt: P0C0Y9*PLUS
#3: Protein
ReactioncenterproteinHchain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit
Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS
Resolution: 2.5→2.54 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3889 / % possible all: 99
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Processing
Software
Name
Version
Classification
REFMAC
5.1.9999
refinement
DENZO
datareduction
SCALEPACK
datascaling
AMoRE
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→23.34 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 9.905 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: TLS thermal mode followed by the restrained refinement of atomic coordinates and isotropic B-factors Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.161 / ESU R Free: 0.146 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the limited electron density quality some atoms at the end of the carbohydrate tails of ligands U10 and CDL were not modelled.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18188
3918
5 %
RANDOM
Rwork
0.15541
-
-
-
all
0.15672
78682
-
-
obs
0.15672
74764
99.12 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 52.933 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.87 Å2
0.44 Å2
0 Å2
2-
-
0.87 Å2
0 Å2
3-
-
-
-1.31 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→23.34 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6474
0
688
243
7405
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
7473
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
7003
X-RAY DIFFRACTION
r_angle_refined_deg
1.686
2.025
10213
X-RAY DIFFRACTION
r_angle_other_deg
1.322
3
16165
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.699
5
818
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.024
22.699
289
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.258
15
985
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.303
15
32
X-RAY DIFFRACTION
r_chiral_restr
0.106
0.2
1023
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
7978
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1569
X-RAY DIFFRACTION
r_nbd_refined
0.2
0.2
1214
X-RAY DIFFRACTION
r_nbd_other
0.172
0.2
5894
X-RAY DIFFRACTION
r_nbtor_other
0.09
0.2
3594
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.12
0.2
173
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.078
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.295
0.2
10
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.054
0.2
2
X-RAY DIFFRACTION
r_mcbond_it
0.907
1.5
5237
X-RAY DIFFRACTION
r_mcbond_other
0.146
1.5
1697
X-RAY DIFFRACTION
r_mcangle_it
1.107
2
6525
X-RAY DIFFRACTION
r_scbond_it
1.714
3
4309
X-RAY DIFFRACTION
r_scangle_it
2.51
4.5
3677
LS refinement shell
Resolution: 2.5→2.564 Å / Total num. of bins used: 20
Rfactor
Num. reflection
Rfree
0.268
295
Rwork
0.232
5435
obs
-
5435
Refinement TLS params.
Method: refined / Origin x: 11.3247 Å / Origin y: 105.5932 Å / Origin z: 34.8431 Å
11
12
13
21
22
23
31
32
33
T
-0.0181 Å2
0.0754 Å2
-0.007 Å2
-
-0.2362 Å2
0.0017 Å2
-
-
-0.1537 Å2
L
1.4068 °2
-0.3473 °2
-0.4882 °2
-
0.9336 °2
0.3368 °2
-
-
1.1894 °2
S
0.0804 Å °
0.1411 Å °
0.06 Å °
-0.0913 Å °
-0.0141 Å °
-0.0786 Å °
-0.1173 Å °
0.0225 Å °
-0.0663 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
L
1 - 281
2
X-RAY DIFFRACTION
1
M
1 - 302
3
X-RAY DIFFRACTION
1
H
11 - 250
4
X-RAY DIFFRACTION
1
M
501 - 502
5
X-RAY DIFFRACTION
1
L
302 - 304
6
X-RAY DIFFRACTION
1
M
401
7
X-RAY DIFFRACTION
1
L
402
8
X-RAY DIFFRACTION
1
M
500
9
X-RAY DIFFRACTION
1
M
503
10
X-RAY DIFFRACTION
1
L
502
11
X-RAY DIFFRACTION
1
M
706
12
X-RAY DIFFRACTION
1
L
707
13
X-RAY DIFFRACTION
1
M
800
14
X-RAY DIFFRACTION
1
H
901
15
X-RAY DIFFRACTION
1
M
902 - 920
16
X-RAY DIFFRACTION
1
H
902 - 1016
17
X-RAY DIFFRACTION
1
M
921 - 994
18
X-RAY DIFFRACTION
1
L
708 - 761
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