1m57

Structure of cytochrome c oxidase from Rhodobacter sphaeroides (EQ(I-286) mutant))

Method: X-RAY DIFFRACTION D_max: 162.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m57
沉积日期 deposition_date	2002-07-08
结构标题 title	Structure of cytochrome c oxidase from Rhodobacter sphaeroides (EQ(I-286) mutant))
关键词 keywords	Membrane Protein, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier	47.16 Å
回转半径 Rg (电子) rg_electron	46.94 Å
零角强度 I(0) i0	789285000.00
分子量 molecular_weight	261620.0 kDa
排除体积 excluded_volume	337920 Å³
包络体积 envelope_volume	402800 Å³
水化壳体积 shell_volume	72692 Å³
包络直径 envelope_diameter	174.0 Å
壳层 Rg shell_rg	49.84 Å
包络 Rg envelope_rg	46.73 Å
形状 Rg shape_rg	46.96 Å
总 Rg total_rg	46.98 Å
总原子数 total_atoms	18498
残基数 n_residues	2228
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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

最大尺寸 Dmax dmax	162.5 Å
Rg (实空间) rg_real	47.59 Å
Rg 误差 (实空间) rg_real_error	2.04 Å
I(0) (实空间) i0_real	7.8930e+08
I(0) 误差 (实空间) i0_real_error	1.6370e+07
Rg (倒空间) rg_reciprocal	47.16 Å
I(0) (倒空间) i0_reciprocal	788900000.0000
解质量估计 total_estimate	0.8274
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	44.3 Å
偏度 Skewness skewness	0.527
峰度 Kurtosis kurtosis	-0.321
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	141700000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; Smooth: 0.559

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

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5. 实体与聚合体信息 (10)

Entity 1 polymer

描述 description	CYTOCHROME C OXIDASE
分子量 formula_weight	63194.4 kDa
EC 编号 ec_number	1.9.3.1
突变 mutation	E286Q
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,G
原子数 atom_count	18934

MADAAIHGHEHDRRGFFTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPQVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTFEQLPKREDWERAPAH

来源 Source

来源生物 organism	Rhodobacter sphaeroides
NCBI 分类编号 ncbi_taxonomy_id	1063
宿主生物 host_organism	Rhodobacter sphaeroides

Entity 2 polymer

描述 description	CYTOCHROME C OXIDASE
分子量 formula_weight	29385.4 kDa
EC 编号 ec_number	1.9.3.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,H

QQQSLEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQARGGTYEL

来源 Source

来源生物 organism	Rhodobacter sphaeroides
NCBI 分类编号 ncbi_taxonomy_id	1063
宿主生物 host_organism	Rhodobacter sphaeroides

Entity 3 polymer

描述 description	CYTOCHROME C OXIDASE
分子量 formula_weight	30197.2 kDa
EC 编号 ec_number	1.9.3.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,I

MAHAKNHDYHILPPSIWPFMASVGAFVMLFGAVLWMHGSGPWMGLIGLVVVLYTMFGWWSDVVTESLEGDHTPVVRLGLRWGFILFIMSEVMFFSAWFWSFFKHALYPMGPESPIIDGIFPPEGIITFDPWHLPLINTLILLCSGCAATWAHHALVHENNRRDVAWGLALAIALGALFTVFQAYEYSHAAFGFAGNIYGANFFMATGFHGFHVIVGTIFLLVCLIRVQRGHFTPEKHVGFEAAIWYWHFVDVVWLFLFASIYIWGQ

来源 Source

来源生物 organism	Rhodobacter sphaeroides
NCBI 分类编号 ncbi_taxonomy_id	1063
宿主生物 host_organism	Rhodobacter sphaeroides

Entity 4 polymer

描述 description	CYTOCHROME C OXIDASE
分子量 formula_weight	5409.3 kDa
EC 编号 ec_number	1.9.3.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,J

MADHSHPAHGHVAGSMDITQQEKTFAGFVRMVTWAAVVIVAALIFLALANA

来源 Source

来源生物 organism	Rhodobacter sphaeroides
NCBI 分类编号 ncbi_taxonomy_id	1063
宿主生物 host_organism	Rhodobacter sphaeroides

Entity 5 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 6 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 non-polymer

描述 description	HEME-A
分子量 formula_weight	852.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 9 non-polymer

描述 description	1,2-Distearoyl-sn-glycerophosphoethanolamine
分子量 formula_weight	748.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 10 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	436

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6. 折叠分类 (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1m57a_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.24 — Cytochrome c oxidase subunit I-like
超家族 Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
家族 Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

结构域编号 domain_id	d1m57b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

结构域编号 domain_id	d1m57b2
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.17 — Transmembrane helix hairpin
超家族 Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
家族 Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

结构域编号 domain_id	d1m57c_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.25 — Cytochrome c oxidase subunit III-like
超家族 Superfamily superfamily	f.25.1 — Cytochrome c oxidase subunit III-like
家族 Family family	f.25.1.1 — Cytochrome c oxidase subunit III-like

结构域编号 domain_id	d1m57d_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.23 — Single transmembrane helix
超家族 Superfamily superfamily	f.23.8 — Bacterial aa3 type cytochrome c oxidase subunit IV
家族 Family family	f.23.8.1 — Bacterial aa3 type cytochrome c oxidase subunit IV

结构域编号 domain_id	d1m57g_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.24 — Cytochrome c oxidase subunit I-like
超家族 Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
家族 Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

结构域编号 domain_id	d1m57h1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

结构域编号 domain_id	d1m57h2
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.17 — Transmembrane helix hairpin
超家族 Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
家族 Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

结构域编号 domain_id	d1m57i_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.25 — Cytochrome c oxidase subunit III-like
超家族 Superfamily superfamily	f.25.1 — Cytochrome c oxidase subunit III-like
家族 Family family	f.25.1.1 — Cytochrome c oxidase subunit III-like

结构域编号 domain_id	d1m57j_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.23 — Single transmembrane helix
超家族 Superfamily superfamily	f.23.8 — Bacterial aa3 type cytochrome c oxidase subunit IV
家族 Family family	f.23.8.1 — Bacterial aa3 type cytochrome c oxidase subunit IV

CATH v4.4 (12 domains)

结构域编号 domain_id	1m57A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	210 — Cytochrome C Oxidase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

结构域编号 domain_id	1m57B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	90 —

结构域编号 domain_id	1m57B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	1m57C01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1m57C02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

结构域编号 domain_id	1m57D00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	160 — Bacterial aa3 type cytochrome c oxidase subunit IV

结构域编号 domain_id	1m57G00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	210 — Cytochrome C Oxidase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

结构域编号 domain_id	1m57H01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	90 —

结构域编号 domain_id	1m57H02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	1m57I01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1m57I02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

结构域编号 domain_id	1m57J00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	160 — Bacterial aa3 type cytochrome c oxidase subunit IV

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7. 引用文献 (1)

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晶胞边长 a length_a	340.720 Å
晶胞边长 b length_b	340.720 Å
晶胞边长 c length_c	89.760 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	H 3
空间群编号 int_tables_number	146
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	4.000 Å
R 因子 r_factor	0.2930
R_work r_work	0.2930
R_free r_free	0.3290

fit	/app/data/saxs_computation/m5/1m57/1m57.fit
pddf	/app/data/pr_computation/m5/1m57/1m57.pr.out
profile	/app/data/saxs_computation/m5/1m57/1m57.dat

Structure of cytochrome c oxidase from Rhodobacter sphaeroides (EQ(I-286) mutant))

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (10)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. 折叠分类 (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)