2fkp

The mutant G127C-T313C of Deinococcus Radiodurans N-acylamino acid racemase

Method: X-RAY DIFFRACTION D_max: 152.7 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2fkp
沉积日期 deposition_date	2006-01-05
结构标题 title	The mutant G127C-T313C of Deinococcus Radiodurans N-acylamino acid racemase
关键词 keywords	N-Acylamino Acid Racemase, Deinococcus Radiodurans, ISOMERASE; ISOMERASE
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	44.31 Å
回转半径 Rg (电子) rg_electron	44.58 Å
零角强度 I(0) i0	379779000.00
分子量 molecular_weight	157340.0 kDa
排除体积 excluded_volume	196050 Å³
包络体积 envelope_volume	259480 Å³
水化壳体积 shell_volume	50754 Å³
包络直径 envelope_diameter	158.0 Å
壳层 Rg shell_rg	46.56 Å
包络 Rg envelope_rg	44.00 Å
形状 Rg shape_rg	44.59 Å
总 Rg total_rg	44.61 Å
总原子数 total_atoms	11068
残基数 n_residues	1440
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	152.7 Å
Rg (实空间) rg_real	44.77 Å
Rg 误差 (实空间) rg_real_error	1.81 Å
I(0) (实空间) i0_real	3.7980e+08
I(0) 误差 (实空间) i0_real_error	7.4500e+06
Rg (倒空间) rg_reciprocal	44.32 Å
I(0) (倒空间) i0_reciprocal	379600000.0000
解质量估计 total_estimate	0.7953
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	38.2 Å
偏度 Skewness skewness	0.520
峰度 Kurtosis kurtosis	-0.430
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	33680000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.702; Smooth: 0.553

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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 (2)

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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	d2fkpa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d2fkpa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d2fkpb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d2fkpb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d2fkpc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d2fkpc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d2fkpd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d2fkpd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2fkpA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	2fkpA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	120 — Enolase-like C-terminal domain

结构域编号 domain_id	2fkpB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	2fkpB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	120 — Enolase-like C-terminal domain

结构域编号 domain_id	2fkpC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	2fkpC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	120 — Enolase-like C-terminal domain

结构域编号 domain_id	2fkpD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	2fkpD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	120 — Enolase-like C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	116.129 Å
晶胞边长 b length_b	116.129 Å
晶胞边长 c length_c	120.536 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	16

空间群 space_group	P 4
空间群编号 int_tables_number	75
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1843
R_work r_work	0.1820
R_free r_free	0.2271

描述 description	N-acylamino acid racemase
分子量 formula_weight	41108.8 kDa
EC 编号 ec_number	5.1.1.10
突变 mutation	G127C,T313C
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	11959

The mutant G127C-T313C of Deinococcus Radiodurans N-acylamino acid racemase

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Deinococcus radiodurans
NCBI 分类编号 ncbi_taxonomy_id	1299
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	891

fit	/app/data/saxs_computation/fk/2fkp/2fkp.fit
pddf	/app/data/pr_computation/fk/2fkp/2fkp.pr.out
profile	/app/data/saxs_computation/fk/2fkp/2fkp.dat