1gmw

Structure of UreE

Method: X-RAY DIFFRACTION D_max: 102.7 Å Quality: REASONABLE

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	1gmw
沉积日期 deposition_date	2001-09-24
结构标题 title	Structure of UreE
关键词 keywords	METALLOCHAPERONE, CHAPERONE; CHAPERONE
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	32.03 Å
回转半径 Rg (电子) rg_electron	31.85 Å
零角强度 I(0) i0	64820800.00
分子量 molecular_weight	61836.0 kDa
排除体积 excluded_volume	76556 Å³
包络体积 envelope_volume	103890 Å³
水化壳体积 shell_volume	29059 Å³
包络直径 envelope_diameter	106.2 Å
壳层 Rg shell_rg	35.86 Å
包络 Rg envelope_rg	31.80 Å
形状 Rg shape_rg	31.87 Å
总 Rg total_rg	32.15 Å
总原子数 total_atoms	4269
残基数 n_residues	536
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	102.7 Å
Rg (实空间) rg_real	32.14 Å
Rg 误差 (实空间) rg_real_error	0.82 Å
I(0) (实空间) i0_real	6.4820e+07
I(0) 误差 (实空间) i0_real_error	9.4420e+05
Rg (倒空间) rg_reciprocal	32.10 Å
I(0) (倒空间) i0_reciprocal	64820000.0000
解质量估计 total_estimate	0.7105
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	37.7 Å
偏度 Skewness skewness	0.350
峰度 Kurtosis kurtosis	-0.548
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4803000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.943; Smooth: 0.894

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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	UREE
分子量 formula_weight	15924.6 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	4433

MLYLTQRLEIPAAATASVTLPIDVRVKSRVKVTLNDGRDAGLLLPRGLLLRGGDVLSNEEGTEFVQVIAADEEVSVVRCDDPFMLAKACYALGNRHVPLQIMPGELRYHHDHVLDDMLRQFGLTVTFGQLPFEPEAGAYASES

来源 Source

来源生物 organism	KLEBSIELLA AEROGENES
NCBI 分类编号 ncbi_taxonomy_id	28451
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	UREE
分子量 formula_weight	15910.6 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

MLYLTQRLEIPAAATASVTLPIDVRVKSRVKVTLNDGRDAGLLLPRGLLLRGGDVLSNEEGTDFVQVIAADEEVSVVRCDDPFMLAKACYALGNRHVPLQIMPGELRYHHDHVLDDMLRQFGLTVTFGQLPFEPEAGAYASES

来源 Source

来源生物 organism	KLEBSIELLA AEROGENES
NCBI 分类编号 ncbi_taxonomy_id	28451
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	164

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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	d1gmwa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.107 — Urease metallochaperone UreE, N-terminal domain
超家族 Superfamily superfamily	b.107.1 — Urease metallochaperone UreE, N-terminal domain
家族 Family family	b.107.1.1 — Urease metallochaperone UreE, N-terminal domain

结构域编号 domain_id	d1gmwa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.38 — Urease metallochaperone UreE, C-terminal domain
家族 Family family	d.58.38.1 — Urease metallochaperone UreE, C-terminal domain

结构域编号 domain_id	d1gmwb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.107 — Urease metallochaperone UreE, N-terminal domain
超家族 Superfamily superfamily	b.107.1 — Urease metallochaperone UreE, N-terminal domain
家族 Family family	b.107.1.1 — Urease metallochaperone UreE, N-terminal domain

结构域编号 domain_id	d1gmwb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.38 — Urease metallochaperone UreE, C-terminal domain
家族 Family family	d.58.38.1 — Urease metallochaperone UreE, C-terminal domain

结构域编号 domain_id	d1gmwc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.107 — Urease metallochaperone UreE, N-terminal domain
超家族 Superfamily superfamily	b.107.1 — Urease metallochaperone UreE, N-terminal domain
家族 Family family	b.107.1.1 — Urease metallochaperone UreE, N-terminal domain

结构域编号 domain_id	d1gmwc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.38 — Urease metallochaperone UreE, C-terminal domain
家族 Family family	d.58.38.1 — Urease metallochaperone UreE, C-terminal domain

结构域编号 domain_id	d1gmwd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.107 — Urease metallochaperone UreE, N-terminal domain
超家族 Superfamily superfamily	b.107.1 — Urease metallochaperone UreE, N-terminal domain
家族 Family family	b.107.1.1 — Urease metallochaperone UreE, N-terminal domain

结构域编号 domain_id	d1gmwd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.38 — Urease metallochaperone UreE, C-terminal domain
家族 Family family	d.58.38.1 — Urease metallochaperone UreE, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1gmwA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	790 — UreE, C-terminal domain

结构域编号 domain_id	1gmwA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	260 — HSP40/DNAj peptide-binding domain
同源超家族 H-superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

结构域编号 domain_id	1gmwB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	790 — UreE, C-terminal domain

结构域编号 domain_id	1gmwB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	260 — HSP40/DNAj peptide-binding domain
同源超家族 H-superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

结构域编号 domain_id	1gmwC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	790 — UreE, C-terminal domain

结构域编号 domain_id	1gmwC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	260 — HSP40/DNAj peptide-binding domain
同源超家族 H-superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

结构域编号 domain_id	1gmwD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	790 — UreE, C-terminal domain

结构域编号 domain_id	1gmwD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	260 — HSP40/DNAj peptide-binding domain
同源超家族 H-superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	43.756 Å
晶胞边长 b length_b	129.905 Å
晶胞边长 c length_c	56.419 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.21 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	1.500 Å
最低分辨率 resolution_low	17.000 Å
R 因子 r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2610

fit	/app/data/saxs_computation/gm/1gmw/1gmw.fit
pddf	/app/data/pr_computation/gm/1gmw/1gmw.pr.out
profile	/app/data/saxs_computation/gm/1gmw/1gmw.dat

Structure of UreE

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 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)