1rg9

S-Adenosylmethionine synthetase complexed with SAM and PPNP

Method: X-RAY DIFFRACTION D_max: 121.4 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	1rg9
沉积日期 deposition_date	2003-11-11
结构标题 title	S-Adenosylmethionine synthetase complexed with SAM and PPNP
关键词 keywords	S-adenosylmethionine synthetase; methionine adenosyltransferase, TRANSFERASE; 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	35.82 Å
回转半径 Rg (电子) rg_electron	35.86 Å
零角强度 I(0) i0	448476000.00
分子量 molecular_weight	170190.0 kDa
排除体积 excluded_volume	211800 Å³
包络体积 envelope_volume	245710 Å³
水化壳体积 shell_volume	55964 Å³
包络直径 envelope_diameter	132.4 Å
壳层 Rg shell_rg	43.22 Å
包络 Rg envelope_rg	36.29 Å
形状 Rg shape_rg	35.89 Å
总 Rg total_rg	36.15 Å
总原子数 total_atoms	11940
残基数 n_residues	1532
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	121.4 Å
Rg (实空间) rg_real	35.89 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	4.4850e+08
I(0) 误差 (实空间) i0_real_error	6.9720e+06
Rg (倒空间) rg_reciprocal	35.85 Å
I(0) (倒空间) i0_reciprocal	448500000.0000
解质量估计 total_estimate	0.8654
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	38.6 Å
偏度 Skewness skewness	0.444
峰度 Kurtosis kurtosis	-0.300
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	166100000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.917

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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 (6)

Entity 1 polymer

描述 description	S-adenosylmethionine synthetase
分子量 formula_weight	41867.3 kDa
EC 编号 ec_number	2.5.1.6
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	11960

AKHLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWVDIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVDRADPLEQGAGDQGLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDGKIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGPMGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCEIQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHPIYKETAAYGHFGREHFPWEKTDKAQLLRDAAGLK

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	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	8

Entity 4 non-polymer

描述 description	S-ADENOSYLMETHIONINE
分子量 formula_weight	398.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	(DIPHOSPHONO)AMINOPHOSPHONIC ACID
分子量 formula_weight	257.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 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	20

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1rg9a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9b3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9c1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9c3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9d1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

结构域编号 domain_id	d1rg9d3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.130 — S-adenosylmethionine synthetase
超家族 Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
家族 Family family	d.130.1.1 — S-adenosylmethionine synthetase

CATH v4.4 (12 domains)

结构域编号 domain_id	1rg9A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rg9D03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	225.820 Å
晶胞边长 b length_b	69.130 Å
晶胞边长 c length_c	118.230 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	16

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	10.000 Å
R 因子 r_factor	0.2120
R_work r_work	0.2110
R_free r_free	0.2410

fit	/app/data/saxs_computation/rg/1rg9/1rg9.fit
pddf	/app/data/pr_computation/rg/1rg9/1rg9.pr.out
profile	/app/data/saxs_computation/rg/1rg9/1rg9.dat