1q90

Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii

Method: X-RAY DIFFRACTION D_max: 124.2 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	1q90
沉积日期 deposition_date	2003-08-22
结构标题 title	Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii
关键词 keywords	;MEMBRANE PROTEIN COMPLEX, PHOTOSYNTHESIS, ELECTRON TRANSFER, OXYDOREDUCTASE, CHLOROPHYLL, BETA-CAROTENE, STIGMATELLIN, SULFOQUINOVOSYLDIACYLGLYCEROL, MONOGALACTOSYLDIACYLGLYCEROL ;; PHOTOSYNTHESIS
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	34.03 Å
回转半径 Rg (电子) rg_electron	33.02 Å
零角强度 I(0) i0	153267000.00
分子量 molecular_weight	110360.0 kDa
排除体积 excluded_volume	142700 Å³
包络体积 envelope_volume	176790 Å³
水化壳体积 shell_volume	45004 Å³
包络直径 envelope_diameter	131.0 Å
壳层 Rg shell_rg	39.32 Å
包络 Rg envelope_rg	33.86 Å
形状 Rg shape_rg	33.04 Å
总 Rg total_rg	33.46 Å
总原子数 total_atoms	7776
残基数 n_residues	952
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	124.2 Å
Rg (实空间) rg_real	34.19 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	1.5330e+08
I(0) 误差 (实空间) i0_real_error	2.3880e+06
Rg (倒空间) rg_reciprocal	34.09 Å
I(0) (倒空间) i0_reciprocal	153300000.0000
解质量估计 total_estimate	0.8221
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.0 Å
偏度 Skewness skewness	0.556
峰度 Kurtosis kurtosis	0.018
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20300000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.642; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.832; Smooth: 0.925

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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 (18)

Entity 1 polymer

描述 description	Apocytochrome f
分子量 formula_weight	32109.8 kDa
突变 mutation	6 His tag at C-terminus
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	7778

YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPARIQGLLVFFSFVLLTQVLLVLKKKQFEKVQLAEMNFHHHHHH

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 2 polymer

描述 description	Cytochrome b6
分子量 formula_weight	24184.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

MSKVYDWFEERLEIQAIADDITSKYVPPHVNIFYCIGGITFTCFLVQVATGFAMTFYYRPTVAEAFASVQYIMTDVNFGWLIRSIHRWSASMMVLMMVLHVFRVYLTGGFKRPRELTWVTGVIMAVCTVSFGVTGYSLPWDQVGYWAVKIVTGVPDAIPGVGGFIVELLRGGVGVGQATLTRFYSLHTFVLPLLTAVFMLMHFLMIRKQGISGPL

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 3 polymer

描述 description	Cytochrome B6-F complex iron-sulfur subunit
分子量 formula_weight	13660.4 kDa
EC 编号 ec_number	1.10.99.1
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

QAAKDALGNDIKAGEWLKTHLAGDRSLSQGLKGDPTYLIVTADSTIEKYGLNAVCTHLGCVVPWVAAENKFKCPCHGSQYNAEGKVVRGPAPLSLALAHCDVAESGLVTFSTWTETDFRTGLEPWWA

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 4 polymer

描述 description	Cytochrome b6-f complex subunit 4
分子量 formula_weight	17305.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

MSVTKKPDLSDPVLKAKLAKGMGHNTYGEPAWPNDLLYMFPVVILGTFACVIGLSVLDPAAMGEPANPFATPLEILPEWYFYPVFQILRVVPNKLLGVLLMAAVPAGLITVPFIESINKFQNPYRRPIATILFLLGTLVAVWLGIGSTFPIDISLTLGL

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 5 polymer

描述 description	Cytochrome B6-F complex iron-sulfur subunit
分子量 formula_weight	4707.3 kDa
EC 编号 ec_number	1.10.99.1
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	R

AASSEVPDMNKRNIMNLILAGGAGLPITTLALGYGAFFVPPSSGGGGGG

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 6 polymer

描述 description	Cytochrome b6f complex subunit petG
分子量 formula_weight	3984.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G

MVEPLLCGIVLGLVPVTIAGLFVTAYLQYLRGDLATY

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 7 polymer

描述 description	Cytochrome b6f complex subunit petL
分子量 formula_weight	3438.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

MLTITSYVGLLIGALVFTLGIYLGLLKVVKLI

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 8 polymer

描述 description	Cytochrome b6f complex subunit PETM
分子量 formula_weight	4037.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	M

GEAEFIAGTALTMVGMTLVGLAIGFVLLRVESLVEEGKI

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 9 polymer

描述 description	Cytochrome b6f complex subunit PETN
分子量 formula_weight	3283.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	N

GEPAIVQIGWAATCVMFSFSLSLVVWGRSGL

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI 分类编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Chlamydomonas reinhardtii

Entity 10 non-polymer

描述 description	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 11 non-polymer

描述 description	BETA-CAROTENE
分子量 formula_weight	536.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 non-polymer

描述 description	EICOSANE
分子量 formula_weight	282.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 13 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 14 non-polymer

描述 description	CHLOROPHYLL A
分子量 formula_weight	893.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 15 non-polymer

描述 description	8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
分子量 formula_weight	418.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 16 non-polymer

描述 description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
分子量 formula_weight	787.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 17 non-polymer

描述 description	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
分子量 formula_weight	795.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 18 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	2

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1q90a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.6 — Cytochrome f, large domain
家族 Family family	b.2.6.1 — Cytochrome f, large domain

结构域编号 domain_id	d1q90a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
家族 Family family	b.84.2.2 — Cytochrome f, small domain

结构域编号 domain_id	d1q90a3
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.23.23 — Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor
家族 Family family	f.23.23.1 — Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor

结构域编号 domain_id	d1q90a4
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1q90b_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.21 — Heme-binding four-helical bundle
超家族 Superfamily superfamily	f.21.1 — Transmembrane di-heme cytochromes
家族 Family family	f.21.1.2 — Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

结构域编号 domain_id	d1q90c_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.33 — ISP domain
超家族 Superfamily superfamily	b.33.1 — ISP domain
家族 Family family	b.33.1.1 — Rieske iron-sulfur protein (ISP)

结构域编号 domain_id	d1q90d_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.32 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
超家族 Superfamily superfamily	f.32.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
家族 Family family	f.32.1.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

结构域编号 domain_id	d1q90g_
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.23.26 — PetG subunit of the cytochrome b6f complex
家族 Family family	f.23.26.1 — PetG subunit of the cytochrome b6f complex

结构域编号 domain_id	d1q90l_
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.23.24 — PetL subunit of the cytochrome b6f complex
家族 Family family	f.23.24.1 — PetL subunit of the cytochrome b6f complex

结构域编号 domain_id	d1q90m_
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.23.25 — PetM subunit of the cytochrome b6f complex
家族 Family family	f.23.25.1 — PetM subunit of the cytochrome b6f complex

结构域编号 domain_id	d1q90n_
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.23.27 — PetN subunit of the cytochrome b6f complex
家族 Family family	f.23.27.1 — PetN subunit of the cytochrome b6f complex

结构域编号 domain_id	d1q90r_
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.23.12 — ISP transmembrane anchor
家族 Family family	f.23.12.1 — ISP transmembrane anchor

CATH v4.4 (6 domains)

结构域编号 domain_id	1q90A01
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	830 — Cytochrome f large domain

结构域编号 domain_id	1q90A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	1q90B00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	810 — Cytochrome Bc1 Complex; Chain C
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome Bc1 Complex; Chain C

结构域编号 domain_id	1q90C00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	102 — 3-layer Sandwich
拓扑 Topology topology	10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

结构域编号 domain_id	1q90D01
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	510 — Single helix bin

结构域编号 domain_id	1q90D02
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	980 — plastocyanin oxidoreductase

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7. 引用文献 (2)

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晶胞边长 a length_a	102.454 Å
晶胞边长 b length_b	171.205 Å
晶胞边长 c length_c	351.009 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	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	34.420 Å
R 因子 r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2610

fit	/app/data/saxs_computation/q9/1q90/1q90.fit
pddf	/app/data/pr_computation/q9/1q90/1q90.pr.out
profile	/app/data/saxs_computation/q9/1q90/1q90.dat

Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii

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 (18)

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 polymer

聚合体 Polymer

来源 Source

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 polymer

聚合体 Polymer

来源 Source

Entity 8 polymer

聚合体 Polymer

来源 Source

Entity 9 polymer

聚合体 Polymer

来源 Source

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 non-polymer

Entity 16 non-polymer

Entity 17 non-polymer

Entity 18 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)