1z7e

Crystal structure of full length ArnA

Method: X-RAY DIFFRACTION D_max: 169.0 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	1z7e
沉积日期 deposition_date	2005-03-24
结构标题 title	Crystal structure of full length ArnA
关键词 keywords	Rossmann fold; OB-like fold, 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	53.07 Å
回转半径 Rg (电子) rg_electron	52.81 Å
零角强度 I(0) i0	2689230000.00
分子量 molecular_weight	433250.0 kDa
排除体积 excluded_volume	541530 Å³
包络体积 envelope_volume	792040 Å³
水化壳体积 shell_volume	121940 Å³
包络直径 envelope_diameter	176.1 Å
壳层 Rg shell_rg	58.71 Å
包络 Rg envelope_rg	51.23 Å
形状 Rg shape_rg	52.78 Å
总 Rg total_rg	53.07 Å
总原子数 total_atoms	30556
残基数 n_residues	3839
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	169.0 Å
Rg (实空间) rg_real	52.88 Å
Rg 误差 (实空间) rg_real_error	0.98 Å
I(0) (实空间) i0_real	2.6890e+09
I(0) 误差 (实空间) i0_real_error	5.1740e+07
Rg (倒空间) rg_reciprocal	53.21 Å
I(0) (倒空间) i0_reciprocal	2690000000.0000
解质量估计 total_estimate	0.6374
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	62.0 Å
偏度 Skewness skewness	0.201
峰度 Kurtosis kurtosis	-0.483
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	344900000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 0.007; Positv: 1.000; Valcen: 0.963; Smooth: 0.850

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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)

Entity 1 polymer

描述 description	protein ArnA
分子量 formula_weight	74385.8 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	30556

MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTDNPGEKAFYGSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPHASKAQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQGSRLNSQPACTARRRTRVLILGVNGFIGNHLTERLLREDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVAIATPIEYTRNPLRVFELDFEENLRIIRYCVKYRKRIIFPSTSEVYGMCSDKYFDEDHSNLIVGPVNKPRWIYSVSKQLLDRVIWAYGEKEGLQFTLFRPFNWMGPRLDNLNAARIGSSRAITQLILNLVEGSPIKLIDGGKQKRCFTDIRDGIEALYRIIENAGNRCDGEIINIGNPENEASIEELGEMLLASFEKHPLRHHFPPFAGFRVVESSSYYGKGYQDVEHRKPSIRNAHRCLDWEPKIDMQETIDETLDFFLRTVDLTDKPS

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	;URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID ;
分子量 formula_weight	580.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1z7ea1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.46 — FMT C-terminal domain-like
超家族 Superfamily superfamily	b.46.1 — FMT C-terminal domain-like
家族 Family family	b.46.1.1 — Post formyltransferase domain

结构域编号 domain_id	d1z7ea2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1z7ea3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

结构域编号 domain_id	d1z7eb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.46 — FMT C-terminal domain-like
超家族 Superfamily superfamily	b.46.1 — FMT C-terminal domain-like
家族 Family family	b.46.1.1 — Post formyltransferase domain

结构域编号 domain_id	d1z7eb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1z7eb3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

结构域编号 domain_id	d1z7ec1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.46 — FMT C-terminal domain-like
超家族 Superfamily superfamily	b.46.1 — FMT C-terminal domain-like
家族 Family family	b.46.1.1 — Post formyltransferase domain

结构域编号 domain_id	d1z7ec2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1z7ec3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

结构域编号 domain_id	d1z7ed1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.46 — FMT C-terminal domain-like
超家族 Superfamily superfamily	b.46.1 — FMT C-terminal domain-like
家族 Family family	b.46.1.1 — Post formyltransferase domain

结构域编号 domain_id	d1z7ed2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1z7ed3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

结构域编号 domain_id	d1z7ee1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.46 — FMT C-terminal domain-like
超家族 Superfamily superfamily	b.46.1 — FMT C-terminal domain-like
家族 Family family	b.46.1.1 — Post formyltransferase domain

结构域编号 domain_id	d1z7ee2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1z7ee3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

结构域编号 domain_id	d1z7ef1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.46 — FMT C-terminal domain-like
超家族 Superfamily superfamily	b.46.1 — FMT C-terminal domain-like
家族 Family family	b.46.1.1 — Post formyltransferase domain

结构域编号 domain_id	d1z7ef2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d1z7ef3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.65 — Formyltransferase
超家族 Superfamily superfamily	c.65.1 — Formyltransferase
家族 Family family	c.65.1.1 — Formyltransferase

CATH v4.4 (12 domains)

结构域编号 domain_id	1z7eA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	12230 —

结构域编号 domain_id	1z7eA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1z7eB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	12230 —

结构域编号 domain_id	1z7eB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1z7eC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	12230 —

结构域编号 domain_id	1z7eC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1z7eD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	12230 —

结构域编号 domain_id	1z7eD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1z7eE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	12230 —

结构域编号 domain_id	1z7eE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1z7eF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	12230 —

结构域编号 domain_id	1z7eF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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7. 引用文献 (1)

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晶胞边长 a length_a	151.689 Å
晶胞边长 b length_b	166.227 Å
晶胞边长 c length_c	261.992 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	24

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2251
R_work r_work	0.2250
R_free r_free	0.2470

fit	/app/data/saxs_computation/z7/1z7e/1z7e.fit
pddf	/app/data/pr_computation/z7/1z7e/1z7e.pr.out
profile	/app/data/saxs_computation/z7/1z7e/1z7e.dat