1f1h

CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH THALLIUM IONS

Method: X-RAY DIFFRACTION D_max: 167.0 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	1f1h
沉积日期 deposition_date	2000-05-19
结构标题 title	CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH THALLIUM IONS
关键词 keywords	GLUTAMINE SYNTHETASE, THALLIUM IONS, LIGASE; LIGASE
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	54.37 Å
回转半径 Rg (电子) rg_electron	54.04 Å
零角强度 I(0) i0	5967500000.00
分子量 molecular_weight	632720.0 kDa
排除体积 excluded_volume	780940 Å³
包络体积 envelope_volume	1020600 Å³
水化壳体积 shell_volume	144310 Å³
包络直径 envelope_diameter	159.1 Å
壳层 Rg shell_rg	67.23 Å
包络 Rg envelope_rg	52.66 Å
形状 Rg shape_rg	54.04 Å
总 Rg total_rg	54.28 Å
总原子数 total_atoms	44112
残基数 n_residues	5616
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	167.0 Å
Rg (实空间) rg_real	53.98 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	5.9670e+09
I(0) 误差 (实空间) i0_real_error	1.1710e+08
Rg (倒空间) rg_reciprocal	54.69 Å
I(0) (倒空间) i0_reciprocal	5974000000.0000
解质量估计 total_estimate	0.8870
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	74.9 Å
偏度 Skewness skewness	-0.048
峰度 Kurtosis kurtosis	-0.593
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	436500000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.923

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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	PROTEIN (GLUTAMINE SYNTHETASE)
分子量 formula_weight	51744.4 kDa
EC 编号 ec_number	6.3.1.2
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	45564

SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGINESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGIADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYFPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKYVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGGVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRFPDPAANPYLCFAALLMAGLDGIKNKIHPGEPMDKNLYDLPPEEAKEIPQVAGSLEEALNALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

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	12

Entity 4 non-polymer

描述 description	THALLIUM (I) ION
分子量 formula_weight	204.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

Entity 5 non-polymer

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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	1452

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6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

结构域编号 domain_id	d1f1ha1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1ha2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hb1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hb2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hc1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hc2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hd1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hd2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1he1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1he2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hf1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hf2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hg1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hg2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hh1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hh2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hi1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hi2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hj1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hj2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hk1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hk2
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.128.1.1 — Glutamine synthetase catalytic domain

结构域编号 domain_id	d1f1hl1
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.15.9.1 — Glutamine synthetase, N-terminal domain

结构域编号 domain_id	d1f1hl2
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.128.1.1 — Glutamine synthetase catalytic domain

CATH v4.4 (24 domains)

结构域编号 domain_id	1f1hA01
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	1f1hA02
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	1f1hB01
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	1f1hB02
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	1f1hC01
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	1f1hC02
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	1f1hD01
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	1f1hD02
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	1f1hE01
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	1f1hE02
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	1f1hF01
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	1f1hF02
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	1f1hG01
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	1f1hG02
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	1f1hH01
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	1f1hH02
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	1f1hI01
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	1f1hI02
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	1f1hJ01
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	1f1hJ02
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	1f1hK01
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	1f1hK02
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	1f1hL01
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	1f1hL02
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

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7. 引用文献 (1)

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晶胞边长 a length_a	231.130 Å
晶胞边长 b length_b	132.790 Å
晶胞边长 c length_c	196.780 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.44 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	48

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	2.670 Å
最低分辨率 resolution_low	32.000 Å
R 因子 r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2630