SAXSdb — 2bv3

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bv3
沉积日期 deposition_date	2005-06-22
结构标题 title	Crystal structure of a mutant elongation factor G trapped with a GTP analogue
关键词 keywords	SWITCH II, ELONGATION FACTOR, GTP-BINDING, TRANSLATION MUTATION THR84ALA, PROTEIN BIOSYNTHESIS; ELONGATION FACTOR
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	31.69 Å
回转半径 Rg (电子) rg_electron	31.77 Å
零角强度 I(0) i0	76540500.00
分子量 molecular_weight	69366.0 kDa
排除体积 excluded_volume	87046 Å³
包络体积 envelope_volume	114050 Å³
水化壳体积 shell_volume	32475 Å³
包络直径 envelope_diameter	120.0 Å
壳层 Rg shell_rg	35.51 Å
包络 Rg envelope_rg	31.67 Å
形状 Rg shape_rg	31.79 Å
总 Rg total_rg	32.04 Å
总原子数 total_atoms	4881
残基数 n_residues	632
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	113.2 Å
Rg (实空间) rg_real	32.03 Å
Rg 误差 (实空间) rg_real_error	1.11 Å
I(0) (实空间) i0_real	7.6540e+07
I(0) 误差 (实空间) i0_real_error	1.4170e+06
Rg (倒空间) rg_reciprocal	31.89 Å
I(0) (倒空间) i0_reciprocal	76530000.0000
解质量估计 total_estimate	0.8321
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	31.7 Å
偏度 Skewness skewness	0.622
峰度 Kurtosis kurtosis	0.046
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13030000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.713; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.847; Smooth: 0.828

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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	ELONGATION FACTOR G
分子量 formula_weight	76756.8 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	A
原子数 atom_count	5038

MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDAPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEESPTFSVSTHPETGSTIISGMGELSLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIKGQ

来源 Source

来源生物 organism	THERMUS THERMOPHILUS
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
分子量 formula_weight	522.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	157

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2bv3a1
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	d2bv3a2
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	d2bv3a3
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	d2bv3a4
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	d2bv3a5
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

CATH v4.4 (5 domains)

结构域编号 domain_id	2bv3A01
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	2bv3A02
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	2bv3A03
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	2bv3A04
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	2bv3A05
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 —

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7. 引用文献 (7)

Crystal Structure of a Mutant Elongation Factor G Trapped with a GTP Analogue.

FEBS Lett. (2005)

PMID: 16083884 · DOI: 10.1016/J.FEBSLET.2005.07.016 PRIMARY

Structural Insights Into Fusidic Acid Resistance and Sensitivity in EF-G

J.Mol.Biol. (2005)

PMID: 15843024 · DOI: 10.1016/J.JMB.2005.02.066

Mutations in the G-Domain of Elongation Factor G from Thermus Thermophilus Affect Both its Interaction with GTP and Fusidic Acid.

J.Biol.Chem. (2001)

PMID: 11371559 · DOI: 10.1074/JBC.M102023200

Structure of a Mutant EF-G Reveals Domain III and Possibly the Fusidic Acid Binding Site

J.Mol.Biol. (2000)

PMID: 11054294 · DOI: 10.1006/JMBI.2000.4168

The Structure of Elongation Factor G in Complex with Gdp: Conformational Flexibility and Nucleotide Exchange

Structure (1996)

PMID: 8736554 · DOI: 10.1016/S0969-2126(96)00061-5

The Crystal Structure of Elongation Factor G Complexed with Gdp, at 2.7 A Resolution

Embo J. (1994)

PMID: 8070396

Three-Dimensional Structure of the Ribosomal Translocase: Elongation Factor G from Thermus Thermophilus

Embo J. (1994)

PMID: 8070397

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晶胞边长 a length_a	74.990 Å
晶胞边长 b length_b	103.340 Å
晶胞边长 c length_c	118.910 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	4

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	2.500 Å
最低分辨率 resolution_low	17.430 Å
R 因子 r_factor	0.2050
R_work r_work	0.2020
R_free r_free	0.2700

fit	/app/data/saxs_computation/bv/2bv3/2bv3.fit
pddf	/app/data/pr_computation/bv/2bv3/2bv3.pr.out
profile	/app/data/saxs_computation/bv/2bv3/2bv3.dat

Crystal structure of a mutant elongation factor G trapped with a GTP analogue

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