1w5c

Photosystem II from Thermosynechococcus elongatus

Method: X-RAY DIFFRACTION D_max: 198.4 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	1w5c
沉积日期 deposition_date	2004-08-06
结构标题 title	Photosystem II from Thermosynechococcus elongatus
关键词 keywords	PHOTOSYNTHESIS, WATER OXIDATION, PHOTOSYSTEM, MEMBRANE PROTEIN; 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	57.08 Å
回转半径 Rg (电子) rg_electron	56.31 Å
零角强度 I(0) i0	3624480000.00
分子量 molecular_weight	533710.0 kDa
排除体积 excluded_volume	673660 Å³
包络体积 envelope_volume	955780 Å³
水化壳体积 shell_volume	135540 Å³
包络直径 envelope_diameter	205.6 Å
壳层 Rg shell_rg	62.32 Å
包络 Rg envelope_rg	56.04 Å
形状 Rg shape_rg	56.48 Å
总 Rg total_rg	55.87 Å
总原子数 total_atoms	35258
残基数 n_residues	4616
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	198.4 Å
Rg (实空间) rg_real	57.06 Å
Rg 误差 (实空间) rg_real_error	1.71 Å
I(0) (实空间) i0_real	3.6240e+09
I(0) 误差 (实空间) i0_real_error	6.6890e+07
Rg (倒空间) rg_reciprocal	57.07 Å
I(0) (倒空间) i0_reciprocal	3624000000.0000
解质量估计 total_estimate	0.8601
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	63.8 Å
偏度 Skewness skewness	0.377
峰度 Kurtosis kurtosis	-0.310
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	922600000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.878

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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	PHOTOSYSTEM Q(B) PROTEIN 1
分子量 formula_weight	39762.3 kDa
来源方法 src_method	nat
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	35614

MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFTALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLASAESAPVAMIAPSING

Entity 2 polymer

描述 description	PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN
分子量 formula_weight	56656.5 kDa
来源方法 src_method	nat
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

MGLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSSIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEAWSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPAFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSGIDPELSPEQVEWGFYQKVGDVTTRRKEAV

Entity 3 polymer

描述 description	PHOTOSYSTEM II CP43 PROTEIN
分子量 formula_weight	51666.1 kDa
来源方法 src_method	nat
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

MKTLSSQKRYSPVVTLSSNSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD

Entity 4 polymer

描述 description	PHOTOSYSTEM II REACTION CENTER D2 PROTEIN
分子量 formula_weight	39388.2 kDa
来源方法 src_method	nat
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

MTIAIGRAPAERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL

Entity 5 polymer

描述 description	CYTOCHROME B559 ALPHA SUBUNIT
分子量 formula_weight	9580.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFLEQLK

Entity 6 polymer

描述 description	CYTOCHROME B559 BETA SUBUNIT
分子量 formula_weight	4936.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

TSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR

Entity 7 polymer

描述 description	PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE
分子量 formula_weight	15251.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 8 polymer

描述 description	PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN
分子量 formula_weight	8528.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 9 polymer

描述 description	CYTOCHROME C-550
分子量 formula_weight	18046.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MLKKCVWLAVALCLCLWQFTMGTALAAELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGKVYY

Entity 10 polymer

描述 description	UNASSIGNED SUBUNITS
分子量 formula_weight	30570.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 11 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	70

Entity 12 non-polymer

描述 description	PHEOPHYTIN A
分子量 formula_weight	871.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 13 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 14 non-polymer

描述 description	FE (II) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 15 non-polymer

描述 description	;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ;
分子量 formula_weight	749.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 16 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 17 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	2

Entity 18 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	2

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6. 折叠分类 (SCOP + CATH) 22 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d1w5ca_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5cb_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5cc_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5cd_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5ce_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5cf_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5cg_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5ch_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5ci_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5cj_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5ck_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5cl_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5ct_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

结构域编号 domain_id	d1w5cv_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.5 — Photosystems
超家族 Superfamily superfamily	i.5.1 — Photosystems
家族 Family family	i.5.1.1 — Photosystems

CATH v4.4 (8 domains)

结构域编号 domain_id	1w5cB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	680 — Photosystem II CP47 reaction center protein
同源超家族 H-superfamily homologous superfamily	10 — Photosystem II CP47 reaction center protein

结构域编号 domain_id	1w5cC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	670 — photosystem ii from thermosynechococcus elongatus

结构域编号 domain_id	1w5cE00
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	860 — Photosystem II cytochrome b559, alpha subunit

结构域编号 domain_id	1w5cH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	680 — Photosystem II CP47 reaction center protein
同源超家族 H-superfamily homologous superfamily	10 — Photosystem II CP47 reaction center protein

结构域编号 domain_id	1w5cI02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	670 — photosystem ii from thermosynechococcus elongatus

结构域编号 domain_id	1w5cK00
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	860 — Photosystem II cytochrome b559, alpha subunit

结构域编号 domain_id	1w5cT00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	1w5cV00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

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7. 引用文献 (1)

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晶胞边长 a length_a	127.517 Å
晶胞边长 b length_b	224.612 Å
晶胞边长 c length_c	305.632 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/w5/1w5c/1w5c.fit
pddf	/app/data/pr_computation/w5/1w5c/1w5c.pr.out
profile	/app/data/saxs_computation/w5/1w5c/1w5c.dat

Photosystem II from Thermosynechococcus elongatus

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

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 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 non-polymer

6. 折叠分类 (SCOP + CATH) 22 domains

SCOP 2.08 (14 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)