8g3h

Structure of cobalamin-dependent methionine synthase (MetH) in a resting state

Method: ELECTRON MICROSCOPY D_max: 98.0 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	8g3h
沉积日期 deposition_date	2023-02-07
结构标题 title	Structure of cobalamin-dependent methionine synthase (MetH) in a resting state
关键词 keywords	Methyltransferase, Transferase, Amino-acid biosynthesis, Methionine biosynthesis; TRANSFERASE
实验方法 method	ELECTRON MICROSCOPY

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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	31.13 Å
回转半径 Rg (电子) rg_electron	30.05 Å
零角强度 I(0) i0	132637000.00
分子量 molecular_weight	93028.0 kDa
排除体积 excluded_volume	117210 Å³
包络体积 envelope_volume	143650 Å³
水化壳体积 shell_volume	39314 Å³
包络直径 envelope_diameter	105.7 Å
壳层 Rg shell_rg	37.56 Å
包络 Rg envelope_rg	30.16 Å
形状 Rg shape_rg	30.09 Å
总 Rg total_rg	30.59 Å
总原子数 total_atoms	6541
残基数 n_residues	841
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	98.0 Å
Rg (实空间) rg_real	31.08 Å
Rg 误差 (实空间) rg_real_error	0.63 Å
I(0) (实空间) i0_real	1.3260e+08
I(0) 误差 (实空间) i0_real_error	2.0800e+06
Rg (倒空间) rg_reciprocal	31.10 Å
I(0) (倒空间) i0_reciprocal	132600000.0000
解质量估计 total_estimate	0.8980
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	36.5 Å
偏度 Skewness skewness	0.277
峰度 Kurtosis kurtosis	-0.453
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	40420000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.844

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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 (3)

Entity 1 polymer

描述 description	Methionine synthase
分子量 formula_weight	131312.3 kDa
EC 编号 ec_number	2.1.1.13
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	6541

MVEVHTCSPGCRHHLGGAGWGDAPLLRLGYNKEARARRFPYLRALSQRVLVFDGAMGTELQKRDLTPEDYGEEAYYGCPEVLNRTRPDVVREIHLSYLEAGAEVIETNSFGALRHVLAEYGLGEEAEELAYRAARIAKEAAEPYGAFVAGALGPGTKLVSLGQISWEELFSAYKEAVRGLVRGGVDLILLETAQDILQVRCAVLAAREAMAELGVELPLQVQVTFEATGTMLVGTDEQAALAALESLPIDVVGMNCATGPDLMDAKIRYFAQESTRFVACLPNAGLPRNEGGRVVYDLTPEELARWHLKFVTEYGVNAVGGCCGTGPEHIRKVAEAVGGRPSPVHKTAFPPQVASLYQAVPLRQETSLLLVGERLNATGSKRFRELLFAGDLEGILALAQEQVAEGAHVLDLSVAWTGRDELEDMKRVLSKLATGVTVPFMVDSTSPEVMEEALKRLPGRAILNSANLEDGLEKFDRVASLAKAHGAALVALAIDEEGMAKTRVKKVEVALRMYERLTEHHGLRPEDLLFDLLTFPITQGDEETRPLARETLLALEELRERLPGVGFVLGVSNVSFGLKPKARRVLNSVFLDEARKKGLTAAIVDAGKILPISQIPEEAYALALDLIYDRREGQDPLFAFIRFFEEHKEVLAEDKEAFQALPVEERLRRRVLEGKRVGLEEDLAEALGRMRPLEIINGPLLEAMKEVGELFGAGKMQLPFVLQAAEVMKQAVAYLEPHMEKKGEGKGKLVLATVKGDVHDIGKNLVDIILTNNGYTVYNLGIKVPIEEMLKAVDEVKPHALGMSGLLVKSTQVMKENLEYMRARGYTLPVILGGAALTRAYVEELRSIYPEVYYAEDAFEGLALMEELTGHRPKDLTLRRARTTRKEAPAPRSKPVSPAPDLPRPPFFGVRVEEGLDLATIAHYVNRLALYRGQWGFSRGGLSREEWEAYVKREADPVFRRLLAEAMAEGWLRPRVLYGFFPVAREGEELWVYSPEGELLEKLRFPRQRGGGISLVDYFRPRFAEPLSDEADWLPGYEEGARDVLGVQLVTMGEEPKRKAEALYREGRYQDYLFVHGFAVEMTEALAEYWHKRMRQMWGIAGQDAPEIRRLFQQEYRGARYSFGYPACPDLADQAKLDRLMDFSRIGVRLTENYQLDPEHSTSALVVHHPEARYFSVD

来源 Source

来源生物 organism	Thermus filiformis
NCBI 分类编号 ncbi_taxonomy_id	276
宿主生物 host_organism	Escherichia coli BL21

Entity 2 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	1

Entity 3 non-polymer

描述 description	COBALAMIN
分子量 formula_weight	1330.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8g3hA01
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	330 — Homocysteine-binding-like domain

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	257706

fit	/app/data/saxs_computation/g3/8g3h/8g3h.fit
pddf	/app/data/pr_computation/g3/8g3h/8g3h.pr.out
profile	/app/data/saxs_computation/g3/8g3h/8g3h.dat