SAXSdb — 1wkm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wkm
沉积日期 deposition_date	2004-06-01
结构标题 title	THE PRODUCT BOUND FORM OF THE MN(II)LOADED METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS
关键词 keywords	AMINOPEPTIDASE, HYPERTHERMOPHILE, METHIONINE COMPLEX, Hydrolase; HYDROLASE
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	62.57 Å
回转半径 Rg (电子) rg_electron	64.01 Å
零角强度 I(0) i0	55096100.00
分子量 molecular_weight	66201.0 kDa
排除体积 excluded_volume	84367 Å³
包络体积 envelope_volume	140930 Å³
水化壳体积 shell_volume	18110 Å³
包络直径 envelope_diameter	186.2 Å
壳层 Rg shell_rg	72.61 Å
包络 Rg envelope_rg	58.65 Å
形状 Rg shape_rg	64.00 Å
总 Rg total_rg	64.20 Å
总原子数 total_atoms	4646
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	195.6 Å
Rg (实空间) rg_real	63.74 Å
Rg 误差 (实空间) rg_real_error	2.91 Å
I(0) (实空间) i0_real	5.5100e+07
I(0) 误差 (实空间) i0_real_error	1.3360e+06
Rg (倒空间) rg_reciprocal	61.33 Å
I(0) (倒空间) i0_reciprocal	54860000.0000
解质量估计 total_estimate	0.5441
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	23.5 Å
偏度 Skewness skewness	0.123
峰度 Kurtosis kurtosis	-1.673
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	949100.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.103

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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	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	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4971

MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE

来源 Source

来源生物 organism	Pyrococcus furiosus
NCBI 分类编号 ncbi_taxonomy_id	2261
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	METHIONINE
分子量 formula_weight	149.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	325

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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	d1wkma1
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	d1wkma2
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	d1wkmb1
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	d1wkmb2
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

CATH v4.4 (4 domains)

结构域编号 domain_id	1wkmA01
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	1wkmA02
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	1wkmB01
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	1wkmB02
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 (1)

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晶胞边长 a length_a	112.010 Å
晶胞边长 b length_b	112.010 Å
晶胞边长 c length_c	122.960 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 64
空间群编号 int_tables_number	172
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	28.000 Å
R 因子 r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2520

fit	/app/data/saxs_computation/wk/1wkm/1wkm.fit
pddf	/app/data/pr_computation/wk/1wkm/1wkm.pr.out
profile	/app/data/saxs_computation/wk/1wkm/1wkm.dat

THE PRODUCT BOUND FORM OF THE MN(II)LOADED 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