1zm9

Structure of eEF2-ETA in complex with PJ34

Method: X-RAY DIFFRACTION D_max: 198.2 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	1zm9
沉积日期 deposition_date	2005-05-10
结构标题 title	Structure of eEF2-ETA in complex with PJ34
关键词 keywords	elongation factor, toxin, ADP-ribosylation, BIOSYNTHETIC PROTEIN-TRANSFERASE COMPLEX; BIOSYNTHETIC PROTEIN/TRANSFERASE
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	64.53 Å
回转半径 Rg (电子) rg_electron	65.13 Å
零角强度 I(0) i0	1607520000.00
分子量 molecular_weight	341230.0 kDa
排除体积 excluded_volume	429210 Å³
包络体积 envelope_volume	676010 Å³
水化壳体积 shell_volume	91876 Å³
包络直径 envelope_diameter	217.7 Å
壳层 Rg shell_rg	58.58 Å
包络 Rg envelope_rg	63.26 Å
形状 Rg shape_rg	65.15 Å
总 Rg total_rg	64.91 Å
总原子数 total_atoms	24042
残基数 n_residues	3087
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	198.2 Å
Rg (实空间) rg_real	64.92 Å
Rg 误差 (实空间) rg_real_error	1.60 Å
I(0) (实空间) i0_real	1.6070e+09
I(0) 误差 (实空间) i0_real_error	3.0220e+07
Rg (倒空间) rg_reciprocal	64.12 Å
I(0) (倒空间) i0_reciprocal	1605000000.0000
解质量估计 total_estimate	0.8323
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	74.3 Å
偏度 Skewness skewness	0.372
峰度 Kurtosis kurtosis	-0.527
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41400000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.017

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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	Elongation factor 2
分子量 formula_weight	93549.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E
原子数 atom_count	24042

MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTRKDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL

Entity 2 polymer

描述 description	exotoxin A
分子量 formula_weight	22496.0 kDa
EC 编号 ec_number	2.4.2.36
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	B,D,F

EFLGDGGDVSFSTRGTQNWTVERLLQAHRQLEERGYVFVGYHGTFLEAAQSIVFGGVRARSQDLDAIWRGFYIAGDPALAYGYAQDQEPDARGRIRNGALLRVYVPRSSLPGFYRTSLTLAAPEAAGEVERLIGHPLPLRLDAITGPEEEGGRLETILGWPLAERTVVIPSAIPTDPRNVGGDLDPSSIPDKEQAISALPDYASQPG

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE
分子量 formula_weight	295.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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6. 折叠分类 (SCOP + CATH) 39 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1zm9a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.1 — Elongation factors

结构域编号 domain_id	d1zm9a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1zm9a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.1 — Translational machinery components

结构域编号 domain_id	d1zm9a4
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.58.11 — EF-G C-terminal domain-like
家族 Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

结构域编号 domain_id	d1zm9a5
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.58.11 — EF-G C-terminal domain-like
家族 Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

结构域编号 domain_id	d1zm9b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

结构域编号 domain_id	d1zm9c1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.1 — Elongation factors

结构域编号 domain_id	d1zm9c2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1zm9c3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.1 — Translational machinery components

结构域编号 domain_id	d1zm9c4
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.58.11 — EF-G C-terminal domain-like
家族 Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

结构域编号 domain_id	d1zm9c5
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.58.11 — EF-G C-terminal domain-like
家族 Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

结构域编号 domain_id	d1zm9d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

结构域编号 domain_id	d1zm9e1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.1 — Elongation factors

结构域编号 domain_id	d1zm9e2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1zm9e3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.1 — Translational machinery components

结构域编号 domain_id	d1zm9e4
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.58.11 — EF-G C-terminal domain-like
家族 Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

结构域编号 domain_id	d1zm9e5
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.58.11 — EF-G C-terminal domain-like
家族 Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

结构域编号 domain_id	d1zm9f_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

CATH v4.4 (21 domains)

结构域编号 domain_id	1zm9A01
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1zm9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1430 — Yeast translation eEF2 (G' domain)
同源超家族 H-superfamily homologous superfamily	10 — Yeast translation eEF2 (G' domain)

结构域编号 domain_id	1zm9A03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	1zm9A04
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	870 — Elongation Factor G (Translational Gtpase), domain 3

结构域编号 domain_id	1zm9A05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1zm9A06
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	240 —

结构域编号 domain_id	1zm9B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	175 — Diphtheria Toxin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Diphtheria Toxin, domain 1

结构域编号 domain_id	1zm9C01
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1zm9C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1430 — Yeast translation eEF2 (G' domain)
同源超家族 H-superfamily homologous superfamily	10 — Yeast translation eEF2 (G' domain)

结构域编号 domain_id	1zm9C03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	1zm9C04
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	870 — Elongation Factor G (Translational Gtpase), domain 3

结构域编号 domain_id	1zm9C05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1zm9C06
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	240 —

结构域编号 domain_id	1zm9D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	175 — Diphtheria Toxin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Diphtheria Toxin, domain 1

结构域编号 domain_id	1zm9E01
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1zm9E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1430 — Yeast translation eEF2 (G' domain)
同源超家族 H-superfamily homologous superfamily	10 — Yeast translation eEF2 (G' domain)

结构域编号 domain_id	1zm9E03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	1zm9E04
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	870 — Elongation Factor G (Translational Gtpase), domain 3

结构域编号 domain_id	1zm9E05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1zm9E06
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	240 —

结构域编号 domain_id	1zm9F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	175 — Diphtheria Toxin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Diphtheria Toxin, domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	330.840 Å
晶胞边长 b length_b	68.740 Å
晶胞边长 c length_c	191.460 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.50 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2550
R_work r_work	0.2540
R_free r_free	0.2740

Structure of eEF2-ETA in complex with PJ34

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 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 39 domains

SCOP 2.08 (18 domains)

CATH v4.4 (21 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/zm/1zm9/1zm9.fit
pddf	/app/data/pr_computation/zm/1zm9/1zm9.pr.out
profile	/app/data/saxs_computation/zm/1zm9/1zm9.dat