1re9

;CRYSTAL STRUCTURE OF CYTOCHROME P450-CAM WITH A FLUORESCENT PROBE D-8-AD (ADAMANTANE-1-CARBOXYLIC ACID-5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO-OCTYL-AMIDE) ;

Method: X-RAY DIFFRACTION D_max: 68.9 Å Quality: EXCELLENT

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	1re9
沉积日期 deposition_date	2003-11-06
结构标题 title	;CRYSTAL STRUCTURE OF CYTOCHROME P450-CAM WITH A FLUORESCENT PROBE D-8-AD (ADAMANTANE-1-CARBOXYLIC ACID-5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO-OCTYL-AMIDE) ;
关键词 keywords	;Monooxygenase, Conformational States, Substrate-linked Sensitizers, SUBSTRATE-BINDING, DANSYL, ADAMANTANE, ADAMANTANE-1-CARBOXYLIC ACID, 4-(5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO)-OCTYL]-AMIDE, CHANNEL, 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	22.43 Å
回转半径 Rg (电子) rg_electron	21.21 Å
零角强度 I(0) i0	35943100.00
分子量 molecular_weight	46793.0 kDa
排除体积 excluded_volume	58713 Å³
包络体积 envelope_volume	66077 Å³
水化壳体积 shell_volume	25479 Å³
包络直径 envelope_diameter	70.3 Å
壳层 Rg shell_rg	28.44 Å
包络 Rg envelope_rg	21.46 Å
形状 Rg shape_rg	21.21 Å
总 Rg total_rg	22.04 Å
总原子数 total_atoms	3292
残基数 n_residues	404
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	68.9 Å
Rg (实空间) rg_real	22.31 Å
Rg 误差 (实空间) rg_real_error	0.31 Å
I(0) (实空间) i0_real	3.5940e+07
I(0) 误差 (实空间) i0_real_error	4.1120e+05
Rg (倒空间) rg_reciprocal	22.34 Å
I(0) (倒空间) i0_reciprocal	35940000.0000
解质量估计 total_estimate	0.9057
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.2 Å
偏度 Skewness skewness	0.165
峰度 Kurtosis kurtosis	-0.481
角度范围 angular_range	— – 0.3550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7109000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.983

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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 (6)

Entity 1 polymer

描述 description	Cytochrome P450-cam
分子量 formula_weight	46588.9 kDa
EC 编号 ec_number	1.14.15.1
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	A
原子数 atom_count	3604

TTETIQSNANLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPDGSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFHGVQLKKGDQILLPQMLSGLDERENACPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV

来源 Source

来源生物 organism	Pseudomonas putida
NCBI 分类编号 ncbi_taxonomy_id	303
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	1

Entity 4 non-polymer

描述 description	ADAMANTANE-1-CARBOXYLIC ACID-5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO-OCTYL-AMIDE
分子量 formula_weight	539.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 6 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	273

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1re9a_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.104 — Cytochrome P450
超家族 Superfamily superfamily	a.104.1 — Cytochrome P450
家族 Family family	a.104.1.1 — Cytochrome P450

CATH v4.4 (1 domains)

结构域编号 domain_id	1re9A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	630 — Cytochrome p450
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome P450

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7. 引用文献 (1)

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晶胞边长 a length_a	64.565 Å
晶胞边长 b length_b	75.941 Å
晶胞边长 c length_c	92.403 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	4

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	1.450 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1621
R_work r_work	0.1598
R_free r_free	0.2183

fit	/app/data/saxs_computation/re/1re9/1re9.fit
pddf	/app/data/pr_computation/re/1re9/1re9.pr.out
profile	/app/data/saxs_computation/re/1re9/1re9.dat