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BMRB: 5333


5333
1IT1
Redox-Coupled Conformational Alternations in Cytochrome c3 from D. vulgaris Miyazaki F on the Basis of its Reduced Solution Structure
Authors
Harada, E., Fukuoka, Y., Ohmura, T., Fukunishi, A., Kawai, G., Fujiwara, T., Akutsu, H.
Assembly
cytochrome c3
Entity
1. cytochrome c3 (polymer, Thiol state: all other bound), 107 monomers, 11529.04 Da Detail

APKAPADGLK MDKTKQPVVF NHSTHKAVKC GDCHHPVNGK EDYQKCATAG CHDNMDKKDK SAKGYYHAMH DKGTKFKSCV GCHLETAGAD AAKKKELTGC KGSKCHS


2. HEM (non-polymer), 616.487 × 4 Da
Total weight
13994.988 Da
Max. entity weight
11529.04 Da
Entity Connection
thioether 8, metal coordination 8 Detail
IDTypeValue orderAtom ID 1Atom ID 2
1thioethersing1:CYS30:SG2:HEM1:CAB
2thioethersing1:CYS46:SG2:HEM1:CAB
3thioethersing1:CYS79:SG2:HEM1:CAB
4thioethersing1:CYS100:SG2:HEM1:CAB
5thioethersing1:CYS33:SG2:HEM1:CAC
6thioethersing1:CYS51:SG2:HEM1:CAC
7thioethersing1:CYS82:SG2:HEM1:CAC
8thioethersing1:CYS105:SG2:HEM1:CAC
9metal coordinationsing1:HIS22:NE22:HEM1:FE
10metal coordinationsing1:HIS34:NE22:HEM1:FE
11metal coordinationsing1:HIS35:NE22:HEM1:FE
12metal coordinationsing1:HIS52:NE22:HEM1:FE
13metal coordinationsing1:HIS25:NE22:HEM1:FE
14metal coordinationsing1:HIS83:NE22:HEM1:FE
15metal coordinationsing1:HIS70:NE22:HEM1:FE
16metal coordinationsing1:HIS106:NE22:HEM1:FE

Source organism
Desulfovibrio vulgaris str. 'Miyazaki F'
Exptl. method
NMR
Refine. method
simulated annealing
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 100.0 %, Completeness: 98.4 %, Completeness (bb): 98.1 % Detail
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Polymer type: polypeptide(L)

Total1H15N
All98.4 % (717 of 729)98.2 % (610 of 621)99.1 % (107 of 108)
Backbone98.1 % (317 of 323)97.7 % (215 of 220)99.0 % (102 of 103)
Sidechain98.5 % (400 of 406)98.5 % (395 of 401)100.0 % (5 of 5)
Aromatic100.0 % (40 of 40)100.0 % (40 of 40)
Methyl97.1 % (33 of 34)97.1 % (33 of 34)

1. cytochrome c3

APKAPADGLK MDKTKQPVVF NHSTHKAVKC GDCHHPVNGK EDYQKCATAG CHDNMDKKDK SAKGYYHAMH DKGTKFKSCV GCHLETAGAD AAKKKELTGC KGSKCHS

Show sample condition
Sample

Temperature 303 (±1) K, pH 7.0 (±0.1)


#NameIsotope labelingTypeConcentration
1cytochrome c3[U-15N]1.0 ~ 2.0 mM

Chem. Shift Complete2
Sequence coverage: 14.0 %, Completeness: 55.4 %, Completeness (bb): 55.6 % Detail
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Polymer type: polypeptide(L)

Total1H15N
All55.4 % (808 of 1458)55.4 % (688 of 1242)55.6 % (120 of 216)
Backbone55.6 % (359 of 646)55.5 % (244 of 440)55.8 % (115 of 206)
Sidechain55.3 % (449 of 812)55.4 % (444 of 802)50.0 % (5 of 10)
Aromatic50.0 % (40 of 80)50.0 % (40 of 80)
Methyl58.8 % (40 of 68)58.8 % (40 of 68)

1. cytochrome c3

APKAPADGLK MDKTKQPVVF NHSTHKAVKC GDCHHPVNGK EDYQKCATAG CHDNMDKKDK SAKGYYHAMH DKGTKFKSCV GCHLETAGAD AAKKKELTGC KGSKCHS

Show sample condition
Sample

Temperature 303 (±1) K, pH 7.0 (±0.1)


#NameIsotope labelingTypeConcentration
1cytochrome c3[U-15N]1.0 ~ 2.0 mM

Chem. Shift Complete3
Sequence coverage: 15.0 %, Completeness: 40.1 %, Completeness (bb): 40.8 % Detail
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Polymer type: polypeptide(L)

Total1H15N
All40.1 % (877 of 2187)39.9 % (743 of 1863)41.4 % (134 of 324)
Backbone40.8 % (395 of 969)40.3 % (266 of 660)41.7 % (129 of 309)
Sidechain39.6 % (482 of 1218)39.7 % (477 of 1203)33.3 % (5 of 15)
Aromatic33.3 % (40 of 120)33.3 % (40 of 120)
Methyl44.1 % (45 of 102)44.1 % (45 of 102)

1. cytochrome c3

APKAPADGLK MDKTKQPVVF NHSTHKAVKC GDCHHPVNGK EDYQKCATAG CHDNMDKKDK SAKGYYHAMH DKGTKFKSCV GCHLETAGAD AAKKKELTGC KGSKCHS

Show sample condition
Sample

Temperature 303 (±1) K, pH 7.0 (±0.1)


#NameIsotope labelingTypeConcentration
1cytochrome c3[U-15N]1.0 ~ 2.0 mM

Chem. Shift Complete4
Sequence coverage: 23.4 %, Completeness: 33.7 %, Completeness (bb): 34.9 % Detail
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Polymer type: polypeptide(L)

Total1H15N
All33.7 % (982 of 2916)33.5 % (833 of 2484)34.5 % (149 of 432)
Backbone34.9 % (451 of 1292)35.0 % (308 of 880)34.7 % (143 of 412)
Sidechain32.4 % (526 of 1624)32.5 % (521 of 1604)25.0 % (5 of 20)
Aromatic27.5 % (44 of 160)27.5 % (44 of 160)
Methyl33.8 % (46 of 136)33.8 % (46 of 136)

1. cytochrome c3

APKAPADGLK MDKTKQPVVF NHSTHKAVKC GDCHHPVNGK EDYQKCATAG CHDNMDKKDK SAKGYYHAMH DKGTKFKSCV GCHLETAGAD AAKKKELTGC KGSKCHS

Show sample condition
Sample

Temperature 303 (±1) K, pH 7.0 (±0.1)


#NameIsotope labelingTypeConcentration
1cytochrome c3[U-15N]1.0 ~ 2.0 mM

Chem. Shift Complete5
Sequence coverage: 14.0 %, Completeness: 28.6 %, Completeness (bb): 30.0 % Detail
Download

Polymer type: polypeptide(L)

Total1H15N
All28.6 % (1041 of 3645)28.3 % (879 of 3105)30.0 % (162 of 540)
Backbone30.0 % (485 of 1615)30.0 % (330 of 1100)30.1 % (155 of 515)
Sidechain27.1 % (551 of 2030)27.2 % (545 of 2005)24.0 % (6 of 25)
Aromatic22.0 % (44 of 200)22.0 % (44 of 200)
Methyl28.2 % (48 of 170)28.2 % (48 of 170)

1. cytochrome c3

APKAPADGLK MDKTKQPVVF NHSTHKAVKC GDCHHPVNGK EDYQKCATAG CHDNMDKKDK SAKGYYHAMH DKGTKFKSCV GCHLETAGAD AAKKKELTGC KGSKCHS

Show sample condition
Sample

Temperature 303 (±1) K, pH 7.0 (±0.1)


#NameIsotope labelingTypeConcentration
1cytochrome c3[U-15N]1.0 ~ 2.0 mM

Protein Blocks Logo
Calculated from 20 models in PDB: 1IT1, Strand ID: A Detail

Release date
2002-06-12
Citation
Redox-coupled conformational alternations in cytochrome c(3) from D. vulgaris Miyazaki F on the basis of its reduced solution structure
Harada, E., Fukuoka, Y., Ohmura, T., Fukunishi, A., Kawai, G., Fujiwara, T., Akutsu, H.
J. Mol. Biol. (2002), 319, 767-778, PubMed 12054869 , DOI 10.1016/S0022-2836(02)00367-4 ,
Related entities 1. cytochrome c3, : 1 : 3 : 3 : 7 : 22 entities Detail
More details for 36 related entities
Experiments performed 5 experiments Detail
nullKeywords Desulfovibrio, cytochrome c3, NMR, structure, oxidation-reduction