2bvc

Crystal structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition state mimic

Method: X-RAY DIFFRACTION D_max: 149.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bvc
沉积日期 deposition_date	2005-06-23
结构标题 title	Crystal structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition state mimic
关键词 keywords	LIGASE, TRANSITION STATE MIMIC, SYNTHETASE; LIGASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	49.52 Å
回转半径 Rg (电子) rg_electron	49.08 Å
零角强度 I(0) i0	1543280000.00
分子量 molecular_weight	323900.0 kDa
排除体积 excluded_volume	402290 Å³
包络体积 envelope_volume	553550 Å³
水化壳体积 shell_volume	89362 Å³
包络直径 envelope_diameter	153.4 Å
壳层 Rg shell_rg	58.26 Å
包络 Rg envelope_rg	47.37 Å
形状 Rg shape_rg	49.06 Å
总 Rg total_rg	49.41 Å
总原子数 total_atoms	22848
残基数 n_residues	2850
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	149.7 Å
Rg (实空间) rg_real	49.26 Å
Rg 误差 (实空间) rg_real_error	1.07 Å
I(0) (实空间) i0_real	1.5430e+09
I(0) 误差 (实空间) i0_real_error	2.6540e+07
Rg (倒空间) rg_reciprocal	49.52 Å
I(0) (倒空间) i0_reciprocal	1544000000.0000
解质量估计 total_estimate	0.8786
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	70.2 Å
偏度 Skewness skewness	0.055
峰度 Kurtosis kurtosis	-0.779
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	483600000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.519

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	GLUTAMINE SYNTHETASE 1
分子量 formula_weight	54584.7 kDa
EC 编号 ec_number	6.3.1.2
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	23469

MAHHHHHHGTEKTPDDVFKLAKDEKVEYVDVRFCDLPGIMQHFTIPASAFDKSVFDDGLAFDGSSIRGFQSIHESDMLLLPDPETARIDPFRAAKTLNINFFVHDPFTLEPYSRDPRNIARKAENYLISTGIADTAYFGAEAEFYIFDSVSFDSRANGSFYEVDAISGWWNTGAATEADGSPNRGYKVRHKGGYFPVAPNDQYVDLRDKMLTNLINSGFILEKGHHEVGSGGQAEINYQFNSLLHAADDMQLYKYIIKNTAWQNGKTVTFMPKPLFGDNGSGMHCHQSLWKDGAPLMYDETGYAGLSDTARHYIGGLLHHAPSLLAFTNPTVNSYKRLVPGYEAPINLVYSQRNRSACVRIPITGSNPKAKRLEFRSPDSSGNPYLAFSAMLMAGLDGIKNKIEPQAPVDKDLYELPPEEAASIPQTPTQLSDVIDRLEADHEYLTEGGVFTNDLIETWISFKRENEIEPVNIRPHPYEFALYYDV

来源 Source

来源生物 organism	MYCOBACTERIUM TUBERCULOSIS
NCBI 分类编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	L-METHIONINE-S-SULFOXIMINE PHOSPHATE
分子量 formula_weight	260.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 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	18

Entity 5 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	621

▼

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2bvca1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
家族 Family family	d.15.9.0 — automated matches

结构域编号 domain_id	d2bvca2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.128 — Glutamine synthetase/guanido kinase
超家族 Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
家族 Family family	d.128.1.0 — automated matches

结构域编号 domain_id	d2bvcb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
家族 Family family	d.15.9.0 — automated matches

结构域编号 domain_id	d2bvcb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.128 — Glutamine synthetase/guanido kinase
超家族 Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
家族 Family family	d.128.1.0 — automated matches

结构域编号 domain_id	d2bvcc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
家族 Family family	d.15.9.0 — automated matches

结构域编号 domain_id	d2bvcc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.128 — Glutamine synthetase/guanido kinase
超家族 Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
家族 Family family	d.128.1.0 — automated matches

结构域编号 domain_id	d2bvcd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
家族 Family family	d.15.9.0 — automated matches

结构域编号 domain_id	d2bvcd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.128 — Glutamine synthetase/guanido kinase
超家族 Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
家族 Family family	d.128.1.0 — automated matches

结构域编号 domain_id	d2bvce1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
家族 Family family	d.15.9.0 — automated matches

结构域编号 domain_id	d2bvce2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.128 — Glutamine synthetase/guanido kinase
超家族 Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
家族 Family family	d.128.1.0 — automated matches

结构域编号 domain_id	d2bvcf1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
家族 Family family	d.15.9.0 — automated matches

结构域编号 domain_id	d2bvcf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.128 — Glutamine synthetase/guanido kinase
超家族 Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
家族 Family family	d.128.1.0 — automated matches

CATH v4.4 (12 domains)

结构域编号 domain_id	2bvcA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	2bvcA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

结构域编号 domain_id	2bvcB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	2bvcB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

结构域编号 domain_id	2bvcC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	2bvcC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

结构域编号 domain_id	2bvcD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	2bvcD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

结构域编号 domain_id	2bvcE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	2bvcE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

结构域编号 domain_id	2bvcF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	2bvcF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	590 — Creatine Kinase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	133.261 Å
晶胞边长 b length_b	229.457 Å
晶胞边长 c length_c	203.167 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	48

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1930
R_work r_work	0.1910
R_free r_free	0.2300

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