2ji2

X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form

Method: X-RAY DIFFRACTION D_max: 96.2 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	2ji2
沉积日期 deposition_date	2007-02-24
结构标题 title	X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form
关键词 keywords	;OXIDOREDUCTASE, RAMAN SPECTROSCOPY, SUPEROXIDE REDUCTASE, INTERMEDIATE TRAPPING, MICROSPECTROPHOTOMETRY, DETOXIFICATION, ELECTRON TRANSPORT, IRON, TRANSPORT, REDOX STATES, METAL-BINDING ;; 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	30.10 Å
回转半径 Rg (电子) rg_electron	29.62 Å
零角强度 I(0) i0	52537500.00
分子量 molecular_weight	56234.0 kDa
排除体积 excluded_volume	69985 Å³
包络体积 envelope_volume	88335 Å³
水化壳体积 shell_volume	25539 Å³
包络直径 envelope_diameter	95.8 Å
壳层 Rg shell_rg	35.89 Å
包络 Rg envelope_rg	29.06 Å
形状 Rg shape_rg	29.62 Å
总 Rg total_rg	30.24 Å
总原子数 total_atoms	3906
残基数 n_residues	502
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	96.2 Å
Rg (实空间) rg_real	30.21 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	5.2540e+07
I(0) 误差 (实空间) i0_real_error	8.3750e+05
Rg (倒空间) rg_reciprocal	30.17 Å
I(0) (倒空间) i0_reciprocal	52540000.0000
解质量估计 total_estimate	0.8716
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	27.2 Å
偏度 Skewness skewness	0.283
峰度 Kurtosis kurtosis	-0.810
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5022000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.843; Smooth: 0.883

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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	Desulfoferrodoxin
分子量 formula_weight	14118.4 kDa
EC 编号 ec_number	1.15.1.2
突变 mutation	E114A
来源方法 src_method	man
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	4534

MPERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVARAYCNIHGHWKAEN

来源 Source

来源生物 organism	Desulfarculus baarsii
NCBI 分类编号 ncbi_taxonomy_id	453230
宿主生物 host_organism	Escherichia coli DH5[alpha]

Entity 2 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	4

Entity 3 non-polymer

描述 description	NITRATE ION
分子量 formula_weight	62.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	4

Entity 5 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 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	568

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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	d2ji2a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.13 — Superoxide reductase-like
家族 Family family	b.1.13.1 — Superoxide reductase-like

结构域编号 domain_id	d2ji2a2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.5 — Rubredoxin-like
家族 Family family	g.41.5.0 — automated matches

结构域编号 domain_id	d2ji2b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.13 — Superoxide reductase-like
家族 Family family	b.1.13.1 — Superoxide reductase-like

结构域编号 domain_id	d2ji2b2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.5 — Rubredoxin-like
家族 Family family	g.41.5.0 — automated matches

结构域编号 domain_id	d2ji2c1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.13 — Superoxide reductase-like
家族 Family family	b.1.13.1 — Superoxide reductase-like

结构域编号 domain_id	d2ji2c2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.5 — Rubredoxin-like
家族 Family family	g.41.5.0 — automated matches

结构域编号 domain_id	d2ji2d1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.13 — Superoxide reductase-like
家族 Family family	b.1.13.1 — Superoxide reductase-like

结构域编号 domain_id	d2ji2d2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.5 — Rubredoxin-like
家族 Family family	g.41.5.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	2ji2A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	100 — Desulphoferrodoxin, N-terminal domain

结构域编号 domain_id	2ji2A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	730 — SOR catalytic domain

结构域编号 domain_id	2ji2B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	100 — Desulphoferrodoxin, N-terminal domain

结构域编号 domain_id	2ji2B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	730 — SOR catalytic domain

结构域编号 domain_id	2ji2C01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	100 — Desulphoferrodoxin, N-terminal domain

结构域编号 domain_id	2ji2C02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	730 — SOR catalytic domain

结构域编号 domain_id	2ji2D01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	100 — Desulphoferrodoxin, N-terminal domain

结构域编号 domain_id	2ji2D02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	730 — SOR catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	70.470 Å
晶胞边长 b length_b	82.870 Å
晶胞边长 c length_c	201.950 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	32

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	47.400 Å
R 因子 r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2220

fit	/app/data/saxs_computation/ji/2ji2/2ji2.fit
pddf	/app/data/pr_computation/ji/2ji2/2ji2.pr.out
profile	/app/data/saxs_computation/ji/2ji2/2ji2.dat