SAXSdb — 1xgm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xgm
沉积日期 deposition_date	1997-11-17
结构标题 title	METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS
关键词 keywords	AMINOPEPTIDASE, HYPERTHERMOPHILE; AMINOPEPTIDASE
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	26.45 Å
回转半径 Rg (电子) rg_electron	25.69 Å
零角强度 I(0) i0	64813300.00
分子量 molecular_weight	65919.0 kDa
排除体积 excluded_volume	83998 Å³
包络体积 envelope_volume	98028 Å³
水化壳体积 shell_volume	31622 Å³
包络直径 envelope_diameter	84.5 Å
壳层 Rg shell_rg	33.45 Å
包络 Rg envelope_rg	25.83 Å
形状 Rg shape_rg	25.64 Å
总 Rg total_rg	26.72 Å
总原子数 total_atoms	4628
残基数 n_residues	590
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	81.9 Å
Rg (实空间) rg_real	26.42 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	6.4810e+07
I(0) 误差 (实空间) i0_real_error	9.1300e+05
Rg (倒空间) rg_reciprocal	26.43 Å
I(0) (倒空间) i0_reciprocal	64810000.0000
解质量估计 total_estimate	0.9019
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	30.0 Å
偏度 Skewness skewness	0.324
峰度 Kurtosis kurtosis	-0.404
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	27860000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.899

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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 (3)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1xgma1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.25 — Methionine aminopeptidase, insert domain

结构域编号 domain_id	d1xgma2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.127 — Creatinase/aminopeptidase
超家族 Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
家族 Family family	d.127.1.1 — Creatinase/aminopeptidase

结构域编号 domain_id	d1xgmb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.25 — Methionine aminopeptidase, insert domain

结构域编号 domain_id	d1xgmb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.127 — Creatinase/aminopeptidase
超家族 Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
家族 Family family	d.127.1.1 — Creatinase/aminopeptidase

CATH v4.4 (4 domains)

结构域编号 domain_id	1xgmA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	230 — Creatine Amidinohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

结构域编号 domain_id	1xgmA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1xgmB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	230 — Creatine Amidinohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

结构域编号 domain_id	1xgmB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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7. 引用文献 (2)

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晶胞边长 a length_a	53.385 Å
晶胞边长 b length_b	85.059 Å
晶胞边长 c length_c	72.705 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.71 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.800 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1810
R_work r_work	0.1810
R_free r_free	0.2630

描述 description	METHIONINE AMINOPEPTIDASE
分子量 formula_weight	32888.4 kDa
EC 编号 ec_number	3.4.11.18
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4638

METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)

描述 description	COBALT (II) ION
分子量 formula_weight	58.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	10

fit	/app/data/saxs_computation/xg/1xgm/1xgm.fit
pddf	/app/data/pr_computation/xg/1xgm/1xgm.pr.out
profile	/app/data/saxs_computation/xg/1xgm/1xgm.dat