1ppj

Bovine cytochrome bc1 complex with stigmatellin and antimycin

Method: X-RAY DIFFRACTION Dmax: 155.4 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1ppj

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1ppj
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1ppj
沉积日期 deposition_date2003-06-16
结构标题 titleBovine cytochrome bc1 complex with stigmatellin and antimycin
关键词 keywords;CYTOCHROME BC1, MEMBRANE PROTEIN, HEME PROTEIN, RIESKE IRON SULFUR PROTEIN, CYTOCHROME B, CYTOCHROME C1, COMPLEX III, MITOCHONDRIAL PROCESSING PROTEASE, MPP UBIQUINONE, OXIDOREDUCTASE, REDOX ENZYME, RESPIRATORY CHAIN, STIGMATELLIN, ANTIMYCIN ;; OXIDOREDUCTASE
实验方法 methodX-RAY DIFFRACTION

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier55.09
回转半径 Rg (电子) rg_electron54.23
零角强度 I(0) i02883880000.00
分子量 molecular_weight457870.0 kDa
排除体积 excluded_volume575410 ų
包络体积 envelope_volume792020 ų
水化壳体积 shell_volume117470 ų
包络直径 envelope_diameter169.9
壳层 Rg shell_rg60.53
包络 Rg envelope_rg53.02
形状 Rg shape_rg54.23
总 Rg total_rg54.38
总原子数 total_atoms32174
残基数 n_residues3993
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax155.4
Rg (实空间) rg_real54.94
Rg 误差 (实空间) rg_real_error1.01
I(0) (实空间) i0_real2.8840e+09
I(0) 误差 (实空间) i0_real_error5.6160e+07
Rg (倒空间) rg_reciprocal55.20
I(0) (倒空间) i0_reciprocal2885000000.0000
解质量估计 total_estimate0.8461
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary64.3
偏度 Skewness skewness0.186
峰度 Kurtosis kurtosis-0.605
角度范围 angular_range— – 0.1450 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha228700000.0000
实空间数据点数 n_real_points30
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.999; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

4. 晶体学与实验 4. Crystallography & Experiment

5. 实体与聚合体信息 (22)

6. 折叠分类 (SCOP + CATH) 57 domains

SCOP 2.08 (30 domains)

结构域编号 domain_idd1ppja1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
家族 Family familyd.185.1.1 — MPP-like
结构域编号 domain_idd1ppja2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
家族 Family familyd.185.1.1 — MPP-like
结构域编号 domain_idd1ppjb1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
家族 Family familyd.185.1.1 — MPP-like
结构域编号 domain_idd1ppjb2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
家族 Family familyd.185.1.1 — MPP-like
结构域编号 domain_idd1ppjc1
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.32 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
超家族 Superfamily superfamilyf.32.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.32.1.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjc2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.21 — Heme-binding four-helical bundle
超家族 Superfamily superfamilyf.21.1 — Transmembrane di-heme cytochromes
家族 Family familyf.21.1.2 — Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjd1
类 Class classa — All alpha proteins
折叠类型 Fold folda.3 — Cytochrome c
超家族 Superfamily superfamilya.3.1 — Cytochrome c
家族 Family familya.3.1.3 — Cytochrome bc1 domain
结构域编号 domain_idd1ppjd2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.11 — Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
家族 Family familyf.23.11.1 — Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
结构域编号 domain_idd1ppje1
类 Class classb — All beta proteins
折叠类型 Fold foldb.33 — ISP domain
超家族 Superfamily superfamilyb.33.1 — ISP domain
家族 Family familyb.33.1.1 — Rieske iron-sulfur protein (ISP)
结构域编号 domain_idd1ppje2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.12 — ISP transmembrane anchor
家族 Family familyf.23.12.1 — ISP transmembrane anchor
结构域编号 domain_idd1ppjf_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.27 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
超家族 Superfamily superfamilyf.27.1 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.27.1.1 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjg_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.13 — Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.23.13.1 — Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjh_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.28 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
超家族 Superfamily superfamilyf.28.1 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.28.1.1 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppji_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.184 — Non-globular alpha+beta subunits of globular proteins
超家族 Superfamily superfamilyd.184.1 — Non-globular alpha+beta subunits of globular proteins
家族 Family familyd.184.1.3 — Ubiquinol-cytochrome c reductase 8 kDa protein
结构域编号 domain_idd1ppjj_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.14 — Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.23.14.1 — Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjn1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
家族 Family familyd.185.1.1 — MPP-like
结构域编号 domain_idd1ppjn2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
家族 Family familyd.185.1.1 — MPP-like
结构域编号 domain_idd1ppjo1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
家族 Family familyd.185.1.1 — MPP-like
结构域编号 domain_idd1ppjo2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
家族 Family familyd.185.1.1 — MPP-like
结构域编号 domain_idd1ppjp1
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.32 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
超家族 Superfamily superfamilyf.32.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.32.1.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjp2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.21 — Heme-binding four-helical bundle
超家族 Superfamily superfamilyf.21.1 — Transmembrane di-heme cytochromes
家族 Family familyf.21.1.2 — Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjq1
类 Class classa — All alpha proteins
折叠类型 Fold folda.3 — Cytochrome c
超家族 Superfamily superfamilya.3.1 — Cytochrome c
家族 Family familya.3.1.3 — Cytochrome bc1 domain
结构域编号 domain_idd1ppjq2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.11 — Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
家族 Family familyf.23.11.1 — Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
结构域编号 domain_idd1ppjr1
类 Class classb — All beta proteins
折叠类型 Fold foldb.33 — ISP domain
超家族 Superfamily superfamilyb.33.1 — ISP domain
家族 Family familyb.33.1.1 — Rieske iron-sulfur protein (ISP)
结构域编号 domain_idd1ppjr2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.12 — ISP transmembrane anchor
家族 Family familyf.23.12.1 — ISP transmembrane anchor
结构域编号 domain_idd1ppjs_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.27 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
超家族 Superfamily superfamilyf.27.1 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.27.1.1 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjt_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.13 — Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.23.13.1 — Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppju_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.28 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
超家族 Superfamily superfamilyf.28.1 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.28.1.1 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
结构域编号 domain_idd1ppjv_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.184 — Non-globular alpha+beta subunits of globular proteins
超家族 Superfamily superfamilyd.184.1 — Non-globular alpha+beta subunits of globular proteins
家族 Family familyd.184.1.3 — Ubiquinol-cytochrome c reductase 8 kDa protein
结构域编号 domain_idd1ppjw_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.23 — Single transmembrane helix
超家族 Superfamily superfamilyf.23.14 — Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family familyf.23.14.1 — Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

CATH v4.4 (27 domains)

结构域编号 domain_id1ppjA01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
结构域编号 domain_id1ppjA02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
结构域编号 domain_id1ppjB01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
结构域编号 domain_id1ppjB02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
结构域编号 domain_id1ppjC00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology810 — Cytochrome Bc1 Complex; Chain C
同源超家族 H-superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
结构域编号 domain_id1ppjD01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
结构域编号 domain_id1ppjD02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c-like domain
结构域编号 domain_id1ppjE01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily270 — Ubiquinol cytochrome reductase, transmembrane domain
结构域编号 domain_id1ppjE02
类 Class class2 — Mainly Beta
架构 Architecture architecture102 — 3-layer Sandwich
拓扑 Topology topology10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
结构域编号 domain_id1ppjF00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1090 — Cytochrome Bc1 Complex; Chain F
同源超家族 H-superfamily homologous superfamily10 — Cytochrome b-c1 complex subunit 7
结构域编号 domain_id1ppjG00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily210 — Cytochrome b-c1 complex subunit 8
结构域编号 domain_id1ppjH00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily20 — Ubiquinol-cytochrome C reductase hinge domain
结构域编号 domain_id1ppjI00
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology210 — Cytochrome Bc1 Complex; Chain I
同源超家族 H-superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain I
结构域编号 domain_id1ppjN01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
结构域编号 domain_id1ppjN02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
结构域编号 domain_id1ppjO01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
结构域编号 domain_id1ppjO02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
结构域编号 domain_id1ppjP00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology810 — Cytochrome Bc1 Complex; Chain C
同源超家族 H-superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
结构域编号 domain_id1ppjQ01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
结构域编号 domain_id1ppjQ02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c-like domain
结构域编号 domain_id1ppjR01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily270 — Ubiquinol cytochrome reductase, transmembrane domain
结构域编号 domain_id1ppjR02
类 Class class2 — Mainly Beta
架构 Architecture architecture102 — 3-layer Sandwich
拓扑 Topology topology10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
结构域编号 domain_id1ppjS00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1090 — Cytochrome Bc1 Complex; Chain F
同源超家族 H-superfamily homologous superfamily10 — Cytochrome b-c1 complex subunit 7
结构域编号 domain_id1ppjT00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily210 — Cytochrome b-c1 complex subunit 8
结构域编号 domain_id1ppjU00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily20 — Ubiquinol-cytochrome C reductase hinge domain
结构域编号 domain_id1ppjV00
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology210 — Cytochrome Bc1 Complex; Chain I
同源超家族 H-superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain I
结构域编号 domain_id1ppjW00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily260 — Cytochrome b-c1 complex subunit 9

7. 引用文献 (1)

8. 文件与曲线 (10)