1xpg

Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Methyltetrahydrofolate

Method: X-RAY DIFFRACTION D_max: 112.5 Å Quality: EXCELLENT

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	1xpg
沉积日期 deposition_date	2004-10-08
结构标题 title	Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Methyltetrahydrofolate
关键词 keywords	TIM barrel, zinc, homocysteine, methyltetrahydrofolate, 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	35.59 Å
回转半径 Rg (电子) rg_electron	34.80 Å
零角强度 I(0) i0	408581000.00
分子量 molecular_weight	167720.0 kDa
排除体积 excluded_volume	210500 Å³
包络体积 envelope_volume	256530 Å³
水化壳体积 shell_volume	58895 Å³
包络直径 envelope_diameter	113.2 Å
壳层 Rg shell_rg	43.26 Å
包络 Rg envelope_rg	34.56 Å
形状 Rg shape_rg	34.80 Å
总 Rg total_rg	35.38 Å
总原子数 total_atoms	11731
残基数 n_residues	1434
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	112.5 Å
Rg (实空间) rg_real	35.41 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	4.0860e+08
I(0) 误差 (实空间) i0_real_error	7.0610e+06
Rg (倒空间) rg_reciprocal	35.52 Å
I(0) (倒空间) i0_reciprocal	408600000.0000
解质量估计 total_estimate	0.9014
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.5 Å
偏度 Skewness skewness	0.161
峰度 Kurtosis kurtosis	-0.542
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	156100000.0000
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: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.959

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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	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
分子量 formula_weight	89991.3 kDa
EC 编号 ec_number	2.1.1.14
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	11993

MHHHHHHGKPIPNPLLGLDSTENLYFQGIDPFTKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFDLPNVSFEDFAVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMREKFA

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
分子量 formula_weight	459.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	MESO-ERYTHRITOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	262

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6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	1xpgA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	210 —

结构域编号 domain_id	1xpgA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	210 —

结构域编号 domain_id	1xpgB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	210 —

结构域编号 domain_id	1xpgB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	210 —

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7. 引用文献 (1)

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晶胞边长 a length_a	163.948 Å
晶胞边长 b length_b	159.303 Å
晶胞边长 c length_c	64.449 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.590 Å
最低分辨率 resolution_low	19.990 Å
R 因子 r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2480

fit	/app/data/saxs_computation/xp/1xpg/1xpg.fit
pddf	/app/data/pr_computation/xp/1xpg/1xpg.pr.out
profile	/app/data/saxs_computation/xp/1xpg/1xpg.dat