1izl

Crystal Structure of Photosystem II

Method: X-RAY DIFFRACTION D_max: 198.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1izl
沉积日期 deposition_date	2002-10-04
结构标题 title	Crystal Structure of Photosystem II
关键词 keywords	;Photosynthesis, Photosynthetic reaction center, Core-antenna, Thermophilic cyanobacterium, Membrane protein complex, Electron transfer, Energy transfer ;; PHOTOSYNTHESIS
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	56.52 Å
回转半径 Rg (电子) rg_electron	56.32 Å
零角强度 I(0) i0	2337800000.00
分子量 molecular_weight	368760.0 kDa
排除体积 excluded_volume	486200 Å³
包络体积 envelope_volume	838710 Å³
水化壳体积 shell_volume	122920 Å³
包络直径 envelope_diameter	201.6 Å
壳层 Rg shell_rg	60.22 Å
包络 Rg envelope_rg	54.67 Å
形状 Rg shape_rg	55.73 Å
总 Rg total_rg	57.92 Å
总原子数 total_atoms	22268
残基数 n_residues	3761
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

▼

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

最大尺寸 Dmax dmax	198.7 Å
Rg (实空间) rg_real	56.58 Å
Rg 误差 (实空间) rg_real_error	1.71 Å
I(0) (实空间) i0_real	2.3380e+09
I(0) 误差 (实空间) i0_real_error	4.7640e+07
Rg (倒空间) rg_reciprocal	56.46 Å
I(0) (倒空间) i0_reciprocal	2337000000.0000
解质量估计 total_estimate	0.8475
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	63.9 Å
偏度 Skewness skewness	0.445
峰度 Kurtosis kurtosis	-0.176
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	1021000000.0000
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: 0.730; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.825

▶

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

▶

5. 实体与聚合体信息 (21)

Entity 1 polymer

描述 description	Photosystem II: Subunit PsbA
分子量 formula_weight	39792.4 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,J
原子数 atom_count	22804

MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWRVVGVWFAALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLASAESAPVAMIAPSING

Entity 2 polymer

描述 description	Photosystem II: Subunit PsbB
分子量 formula_weight	49478.6 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	B,L

MGLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSSIAAVFFAAFVVAGTMWYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSGIDPELSPEQVEWGFYQKVGDVTTRRKEAV

Entity 3 polymer

描述 description	Photosystem II: Subunit PsbC
分子量 formula_weight	49868.9 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	C,M

MKTLSSQKRYSPVVTLSSNSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD

Entity 4 polymer

描述 description	Photosystem II: Subunit PsbD
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,N

MTIAIGRAPAERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL

Entity 5 polymer

描述 description	Photosystem II: Subunit PsbE
分子量 formula_weight	9449.6 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	E,P

AGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFLEQLK

Entity 6 polymer

描述 description	Photosystem II: Subunit PsbF
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,Q

TSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR

Entity 7 polymer

描述 description	Photosystem II: Subunit PsbG
分子量 formula_weight	18741.0 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	G,R

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 8 polymer

描述 description	Photosystem II: Subunit PsbH
分子量 formula_weight	2826.5 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	H,S

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 9 polymer

描述 description	Photosystem II: Subunit PsbI
分子量 formula_weight	2230.7 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	I,T

XXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 10 polymer

描述 description	Photosystem II: Subunit PsbK
分子量 formula_weight	4101.9 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	K,W

KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR

Entity 11 polymer

描述 description	Photosystem II: Subunit PsbO
分子量 formula_weight	17464.5 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	O,Y

Entity 12 polymer

描述 description	Photosystem II: Subunit PsbU
分子量 formula_weight	8273.2 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	U,Z

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 13 polymer

描述 description	Photosystem II: Subunit PsbV
分子量 formula_weight	15148.3 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	V,0

AELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGKVYY

Entity 14 polymer

描述 description	Photosystem II: Subunit PsbX
分子量 formula_weight	2145.6 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,1

XXXXXXXXXXXXXXXXXXXXXXXXX

Entity 15 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 16 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	72

Entity 17 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 18 non-polymer

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

Entity 19 non-polymer

描述 description	2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID
分子量 formula_weight	378.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 20 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 21 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	4

▼

6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (28 domains)

结构域编号 domain_id	d1izl0_
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	d1izl1_
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	d1izla_
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	d1izlb_
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	d1izlc_
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	d1izld_
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	d1izle_
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	d1izlf_
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	d1izlg_
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	d1izlh_
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	d1izli_
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	d1izlj_
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	d1izlk_
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	d1izll_
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	d1izlm_
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	d1izln_
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	d1izlo_
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	d1izlp_
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	d1izlq_
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	d1izlr_
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	d1izls_
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	d1izlt_
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	d1izlu_
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	d1izlv_
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	d1izlw_
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	d1izlx_
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	d1izly_
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	d1izlz_
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 (2 domains)

结构域编号 domain_id	1izl000
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	1izlV00
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	129.377 Å
晶胞边长 b length_b	225.192 Å
晶胞边长 c length_c	308.672 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	3.700 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.5304
R_work r_work	0.5304
R_free r_free	—

fit	/app/data/saxs_computation/iz/1izl/1izl.fit
pddf	/app/data/pr_computation/iz/1izl/1izl.pr.out
profile	/app/data/saxs_computation/iz/1izl/1izl.dat

Crystal Structure of Photosystem II

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 (21)

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 polymer

聚合体 Polymer

Entity 12 polymer

聚合体 Polymer

Entity 13 polymer

聚合体 Polymer

Entity 14 polymer

聚合体 Polymer

Entity 15 non-polymer

Entity 16 non-polymer

Entity 17 non-polymer

Entity 18 non-polymer

Entity 19 non-polymer

Entity 20 non-polymer

Entity 21 non-polymer

6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (28 domains)

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)