1occ

STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE

Method: X-RAY DIFFRACTION Dmax: 170.8 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1occ

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1occ
下载 Download

1. 结构基本信息 1. Structure Basics

条目编号 entry_id1occ
沉积日期 deposition_date1996-04-18
结构标题 titleSTRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE
关键词 keywordsCYTOCHROME C OXIDASE, OXIDOREDUCTASE (CYTOCHROME(C)-OXYGEN); OXIDOREDUCTASE (CYTOCHROME(C)-OXYGEN)
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_guinier50.98
回转半径 Rg (电子) rg_electron50.52
零角强度 I(0) i02105750000.00
分子量 molecular_weight407230.0 kDa
排除体积 excluded_volume517740 ų
包络体积 envelope_volume669030 ų
水化壳体积 shell_volume107580 ų
包络直径 envelope_diameter169.3
壳层 Rg shell_rg56.43
包络 Rg envelope_rg49.80
形状 Rg shape_rg50.48
总 Rg total_rg50.82
总原子数 total_atoms28722
残基数 n_residues3560
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 dmax170.8
Rg (实空间) rg_real50.91
Rg 误差 (实空间) rg_real_error1.61
I(0) (实空间) i0_real2.1060e+09
I(0) 误差 (实空间) i0_real_error4.4770e+07
Rg (倒空间) rg_reciprocal51.03
I(0) (倒空间) i0_reciprocal2106000000.0000
解质量估计 total_estimate0.8828
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary60.6
偏度 Skewness skewness0.275
峰度 Kurtosis kurtosis-0.425
角度范围 angular_range— – 0.1550 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha312800000.0000
实空间数据点数 n_real_points32
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.871

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

5. 实体与聚合体信息 (17)

6. 折叠分类 (SCOP + CATH) 58 domains

SCOP 2.08 (28 domains)

结构域编号 domain_idd1occa_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.24 — Cytochrome c oxidase subunit I-like
超家族 Superfamily superfamilyf.24.1 — Cytochrome c oxidase subunit I-like
家族 Family familyf.24.1.1 — Cytochrome c oxidase subunit I-like
结构域编号 domain_idd1occb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.6 — Cupredoxin-like
超家族 Superfamily superfamilyb.6.1 — Cupredoxins
家族 Family familyb.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II
结构域编号 domain_idd1occb2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.17 — Transmembrane helix hairpin
超家族 Superfamily superfamilyf.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
家族 Family familyf.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region
结构域编号 domain_idd1occc_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.25 — Cytochrome c oxidase subunit III-like
超家族 Superfamily superfamilyf.25.1 — Cytochrome c oxidase subunit III-like
家族 Family familyf.25.1.1 — Cytochrome c oxidase subunit III-like
结构域编号 domain_idd1occd_
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.23.1 — Mitochondrial cytochrome c oxidase subunit IV
家族 Family familyf.23.1.1 — Mitochondrial cytochrome c oxidase subunit IV
结构域编号 domain_idd1occe_
类 Class classa — All alpha proteins
折叠类型 Fold folda.118 — alpha-alpha superhelix
超家族 Superfamily superfamilya.118.11 — Cytochrome c oxidase subunit E
家族 Family familya.118.11.1 — Cytochrome c oxidase subunit E
结构域编号 domain_idd1occf_
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.5 — Rubredoxin-like
家族 Family familyg.41.5.3 — Cytochrome c oxidase Subunit F
结构域编号 domain_idd1occg_
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.23.2 — Mitochondrial cytochrome c oxidase subunit VIa
家族 Family familyf.23.2.1 — Mitochondrial cytochrome c oxidase subunit VIa
结构域编号 domain_idd1occh_
类 Class classa — All alpha proteins
折叠类型 Fold folda.51 — Cytochrome c oxidase subunit h
超家族 Superfamily superfamilya.51.1 — Cytochrome c oxidase subunit h
家族 Family familya.51.1.1 — Cytochrome c oxidase subunit h
结构域编号 domain_idd1occi_
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.23.3 — Mitochondrial cytochrome c oxidase subunit VIc
家族 Family familyf.23.3.1 — Mitochondrial cytochrome c oxidase subunit VIc
结构域编号 domain_idd1occj_
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.23.4 — Mitochondrial cytochrome c oxidase subunit VIIa
家族 Family familyf.23.4.1 — Mitochondrial cytochrome c oxidase subunit VIIa
结构域编号 domain_idd1occk_
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.23.5 — Mitochondrial cytochrome c oxidase subunit VIIb
家族 Family familyf.23.5.1 — Mitochondrial cytochrome c oxidase subunit VIIb
结构域编号 domain_idd1occl_
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.23.6 — Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa)
家族 Family familyf.23.6.1 — Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa)
结构域编号 domain_idd1occm_
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.23.7 — Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)
家族 Family familyf.23.7.1 — Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)
结构域编号 domain_idd1occn_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.24 — Cytochrome c oxidase subunit I-like
超家族 Superfamily superfamilyf.24.1 — Cytochrome c oxidase subunit I-like
家族 Family familyf.24.1.1 — Cytochrome c oxidase subunit I-like
结构域编号 domain_idd1occo1
类 Class classb — All beta proteins
折叠类型 Fold foldb.6 — Cupredoxin-like
超家族 Superfamily superfamilyb.6.1 — Cupredoxins
家族 Family familyb.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II
结构域编号 domain_idd1occo2
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.17 — Transmembrane helix hairpin
超家族 Superfamily superfamilyf.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
家族 Family familyf.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region
结构域编号 domain_idd1occp_
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.25 — Cytochrome c oxidase subunit III-like
超家族 Superfamily superfamilyf.25.1 — Cytochrome c oxidase subunit III-like
家族 Family familyf.25.1.1 — Cytochrome c oxidase subunit III-like
结构域编号 domain_idd1occq_
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.23.1 — Mitochondrial cytochrome c oxidase subunit IV
家族 Family familyf.23.1.1 — Mitochondrial cytochrome c oxidase subunit IV
结构域编号 domain_idd1occr_
类 Class classa — All alpha proteins
折叠类型 Fold folda.118 — alpha-alpha superhelix
超家族 Superfamily superfamilya.118.11 — Cytochrome c oxidase subunit E
家族 Family familya.118.11.1 — Cytochrome c oxidase subunit E
结构域编号 domain_idd1occs_
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.5 — Rubredoxin-like
家族 Family familyg.41.5.3 — Cytochrome c oxidase Subunit F
结构域编号 domain_idd1occt_
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.23.2 — Mitochondrial cytochrome c oxidase subunit VIa
家族 Family familyf.23.2.1 — Mitochondrial cytochrome c oxidase subunit VIa
结构域编号 domain_idd1occu_
类 Class classa — All alpha proteins
折叠类型 Fold folda.51 — Cytochrome c oxidase subunit h
超家族 Superfamily superfamilya.51.1 — Cytochrome c oxidase subunit h
家族 Family familya.51.1.1 — Cytochrome c oxidase subunit h
结构域编号 domain_idd1occv_
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.23.3 — Mitochondrial cytochrome c oxidase subunit VIc
家族 Family familyf.23.3.1 — Mitochondrial cytochrome c oxidase subunit VIc
结构域编号 domain_idd1occw_
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.23.4 — Mitochondrial cytochrome c oxidase subunit VIIa
家族 Family familyf.23.4.1 — Mitochondrial cytochrome c oxidase subunit VIIa
结构域编号 domain_idd1occx_
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.23.5 — Mitochondrial cytochrome c oxidase subunit VIIb
家族 Family familyf.23.5.1 — Mitochondrial cytochrome c oxidase subunit VIIb
结构域编号 domain_idd1occy_
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.23.6 — Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa)
家族 Family familyf.23.6.1 — Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa)
结构域编号 domain_idd1occz_
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.23.7 — Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)
家族 Family familyf.23.7.1 — Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)

CATH v4.4 (30 domains)

结构域编号 domain_id1occA00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology210 — Cytochrome C Oxidase; Chain A
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase-like, subunit I domain
结构域编号 domain_id1occB01
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 superfamily90
结构域编号 domain_id1occB02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
结构域编号 domain_id1occC01
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 superfamily70
结构域编号 domain_id1occC02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily80 — Cytochrome c oxidase, subunit III, four-helix bundle
结构域编号 domain_id1occD00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology442 — Cytochrome C Oxidase; Chain D
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase subunit IV
结构域编号 domain_id1occE00
类 Class class1 — Mainly Alpha
架构 Architecture architecture25 — Alpha Horseshoe
拓扑 Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily40 — Cytochrome c oxidase, subunit Va/VI
结构域编号 domain_id1occF00
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology11 — Cytochrome C Oxidase; Chain F
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase, subunit Vb
结构域编号 domain_id1occG00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology95 — Cytochrome C Oxidase; Chain G
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase, subunit VIa
结构域编号 domain_id1occH00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily140 — Cytochrome c oxidase, subunit VIb
结构域编号 domain_id1occI00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology93 — Cytochrome C Oxidase; Chain I
同源超家族 H-superfamily homologous superfamily10 — Mitochondrial cytochrome c oxidase subunit VIc/VIIs
结构域编号 domain_id1occJ00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology91 — Cytochrome C Oxidase; Chain J
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase, subunit VIIa
结构域编号 domain_id1occK00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology51 — Cytochrome C Oxidase; Chain K
同源超家族 H-superfamily homologous superfamily10 — Cytochrome C Oxidase, chain K
结构域编号 domain_id1occL00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology49 — Cytochrome C Oxidase; Chain L
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase subunit VIIc
结构域编号 domain_id1occM00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology81 — Cytochrome C Oxidase; Chain M
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase, subunit 8
结构域编号 domain_id1occN00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology210 — Cytochrome C Oxidase; Chain A
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase-like, subunit I domain
结构域编号 domain_id1occO01
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 superfamily90
结构域编号 domain_id1occO02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
结构域编号 domain_id1occP01
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 superfamily70
结构域编号 domain_id1occP02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily80 — Cytochrome c oxidase, subunit III, four-helix bundle
结构域编号 domain_id1occQ00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology442 — Cytochrome C Oxidase; Chain D
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase subunit IV
结构域编号 domain_id1occR00
类 Class class1 — Mainly Alpha
架构 Architecture architecture25 — Alpha Horseshoe
拓扑 Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily40 — Cytochrome c oxidase, subunit Va/VI
结构域编号 domain_id1occS00
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology11 — Cytochrome C Oxidase; Chain F
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase, subunit Vb
结构域编号 domain_id1occT00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology95 — Cytochrome C Oxidase; Chain G
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase, subunit VIa
结构域编号 domain_id1occU00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily140 — Cytochrome c oxidase, subunit VIb
结构域编号 domain_id1occV00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology93 — Cytochrome C Oxidase; Chain I
同源超家族 H-superfamily homologous superfamily10 — Mitochondrial cytochrome c oxidase subunit VIc/VIIs
结构域编号 domain_id1occW00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology91 — Cytochrome C Oxidase; Chain J
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase, subunit VIIa
结构域编号 domain_id1occX00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology51 — Cytochrome C Oxidase; Chain K
同源超家族 H-superfamily homologous superfamily10 — Cytochrome C Oxidase, chain K
结构域编号 domain_id1occY00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology49 — Cytochrome C Oxidase; Chain L
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase subunit VIIc
结构域编号 domain_id1occZ00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology81 — Cytochrome C Oxidase; Chain M
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c oxidase, subunit 8

7. 引用文献 (2)

8. 文件与曲线 (10)