1fe1

CRYSTAL STRUCTURE PHOTOSYSTEM II

Method: X-RAY DIFFRACTION D_max: 208.9 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	1fe1
沉积日期 deposition_date	2000-07-20
结构标题 title	CRYSTAL STRUCTURE PHOTOSYSTEM II
关键词 keywords	;PHOTOSYNTHESIS, PHOTOSYNTHETIC REACTION CENTER, CORE- ANTEN A LIGHT-HARVESTING SYSTEM, THERMOPHILIC CYANOBACTERIUM, MEMBRANE PROTEIN, PHOTOSYNTHESIS-ELECTRON TRANSPORT COMPLEX ;; PHOTOSYNTHESIS/ELECTRON TRANSPORT
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	58.49 Å
回转半径 Rg (电子) rg_electron	58.84 Å
零角强度 I(0) i0	1252170000.00
分子量 molecular_weight	297190.0 kDa
排除体积 excluded_volume	573910 Å³
包络体积 envelope_volume	506260 Å³
水化壳体积 shell_volume	76839 Å³
包络直径 envelope_diameter	200.4 Å
壳层 Rg shell_rg	55.42 Å
包络 Rg envelope_rg	55.71 Å
形状 Rg shape_rg	56.26 Å
总 Rg total_rg	59.45 Å
总原子数 total_atoms	1852
残基数 n_residues	—
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	208.9 Å
Rg (实空间) rg_real	58.81 Å
Rg 误差 (实空间) rg_real_error	2.00 Å
I(0) (实空间) i0_real	1.2530e+09
I(0) 误差 (实空间) i0_real_error	2.8710e+07
Rg (倒空间) rg_reciprocal	58.29 Å
I(0) (倒空间) i0_reciprocal	1251000000.0000
解质量估计 total_estimate	0.8540
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	61.9 Å
偏度 Skewness skewness	0.438
峰度 Kurtosis kurtosis	-0.345
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0085
最高正则化参数 α highest_alpha	180700000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.001; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.840

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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 (17)

Entity 1 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBA)
分子量 formula_weight	14400.7 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	A,J
原子数 atom_count	4328

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 2 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBD)
分子量 formula_weight	14826.3 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	B,K

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 3 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBC)
分子量 formula_weight	13294.4 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	C,L

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 4 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBB)
分子量 formula_weight	13209.3 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	D,M

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 5 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBE)
分子量 formula_weight	3422.2 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	E,N

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 6 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBF)
分子量 formula_weight	2571.2 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	F,O

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 7 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT UNKNOWN)
分子量 formula_weight	26570.6 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	G,P

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 8 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBO)
分子量 formula_weight	9805.1 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	H,Q

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 9 polymer

描述 description	PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBV)
分子量 formula_weight	7422.1 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	I,R

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 10 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 11 non-polymer

描述 description	TYROSINE
分子量 formula_weight	181.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 12 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	64

Entity 13 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 14 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 15 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 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	4

Entity 17 non-polymer

描述 description	CADMIUM ION
分子量 formula_weight	112.4 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) 18 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1fe1a_
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	d1fe1b_
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	d1fe1c_
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	d1fe1d_
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	d1fe1e_
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	d1fe1f_
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	d1fe1g_
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	d1fe1h_
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	d1fe1i_
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	d1fe1j_
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	d1fe1k_
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	d1fe1l_
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	d1fe1m_
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	d1fe1n_
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	d1fe1o_
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	d1fe1p_
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	d1fe1q_
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	d1fe1r_
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

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7. 引用文献 (1)

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晶胞边长 a length_a	130.010 Å
晶胞边长 b length_b	226.720 Å
晶胞边长 c length_c	308.290 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	3.800 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/fe/1fe1/1fe1.fit
pddf	/app/data/pr_computation/fe/1fe1/1fe1.pr.out
profile	/app/data/saxs_computation/fe/1fe1/1fe1.dat

CRYSTAL STRUCTURE 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

5. 实体与聚合体信息 (17)

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 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

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (18 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)