2c1u

CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - OXIDISED FORM

Method: X-RAY DIFFRACTION D_max: 123.3 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	2c1u
沉积日期 deposition_date	2005-09-21
结构标题 title	CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - OXIDISED FORM
关键词 keywords	ELECTRON TRANSPORT, HEME, OXIDOREDUCTASE, PERIPLASMIC, PEROXIDASE; 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	37.13 Å
回转半径 Rg (电子) rg_electron	36.38 Å
零角强度 I(0) i0	319933000.00
分子量 molecular_weight	144760.0 kDa
排除体积 excluded_volume	180760 Å³
包络体积 envelope_volume	235910 Å³
水化壳体积 shell_volume	53868 Å³
包络直径 envelope_diameter	134.1 Å
壳层 Rg shell_rg	42.74 Å
包络 Rg envelope_rg	35.88 Å
形状 Rg shape_rg	36.39 Å
总 Rg total_rg	36.77 Å
总原子数 total_atoms	10183
残基数 n_residues	1304
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	123.3 Å
Rg (实空间) rg_real	37.06 Å
Rg 误差 (实空间) rg_real_error	1.04 Å
I(0) (实空间) i0_real	3.1990e+08
I(0) 误差 (实空间) i0_real_error	5.6170e+06
Rg (倒空间) rg_reciprocal	37.11 Å
I(0) (倒空间) i0_reciprocal	319900000.0000
解质量估计 total_estimate	0.8902
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	45.9 Å
偏度 Skewness skewness	0.277
峰度 Kurtosis kurtosis	-0.347
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	58480000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.941

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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 (4)

Entity 1 polymer

描述 description	DI-HAEM CYTOCHROME C PEROXIDASE
分子量 formula_weight	36326.5 kDa
EC 编号 ec_number	1.11.1.5
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	11016

ETEAIDNGALREEAKGVFEAIPEKMTAIKQTEDNPEGVPLTAEKIELGKVLFFDPRMSSSGLISCQTCHNVGLGGVDGLPTSIGHGWQKGPRNAPTMLNAIFNAAQFWDGRAADLAEQAKGPVQAGVEMSNTPDQVVKTINSMPEYVEAFKAAFPEEADPVTFDNFAAAIEQFEATLITPNSAFDRFLAGDDAAMTDQEKRGLQAFMETGCTACHYGVNFGGQDYHPFGLIAKPGAEVLPAGDTGRFEVTRTTDDEYVFRAAPLRNVALTAPYFHSGVVWELAEAVKIMSSAQIGTELTDQQAEDITAFLGTLTGEQPVIDHPILPVRTGTTPLPTPM

Entity 2 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	8

Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	833

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2c1ua1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.0 — automated matches

结构域编号 domain_id	d2c1ua2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.0 — automated matches

结构域编号 domain_id	d2c1ub1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.0 — automated matches

结构域编号 domain_id	d2c1ub2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.0 — automated matches

结构域编号 domain_id	d2c1uc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.0 — automated matches

结构域编号 domain_id	d2c1uc2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.0 — automated matches

结构域编号 domain_id	d2c1ud1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.0 — automated matches

结构域编号 domain_id	d2c1ud2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	2c1uA01
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	2c1uA02
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	2c1uB01
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	2c1uB02
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	2c1uC01
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	2c1uC02
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	2c1uD01
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	2c1uD02
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	78.800 Å
晶胞边长 b length_b	51.100 Å
晶胞边长 c length_c	167.900 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.20 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.950 Å
最低分辨率 resolution_low	29.880 Å
R 因子 r_factor	0.1700
R_work r_work	0.1690
R_free r_free	0.2200

fit	/app/data/saxs_computation/c1/2c1u/2c1u.fit
pddf	/app/data/pr_computation/c1/2c1u/2c1u.pr.out
profile	/app/data/saxs_computation/c1/2c1u/2c1u.dat