2i2x

Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri

Method: X-RAY DIFFRACTION D_max: 187.9 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	2i2x
沉积日期 deposition_date	2006-08-17
结构标题 title	Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri
关键词 keywords	TIM barrel and helix bundle (MtaB); Rossman fold and helix bundle (MtaC), 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	58.78 Å
回转半径 Rg (电子) rg_electron	58.44 Å
零角强度 I(0) i0	5766160000.00
分子量 molecular_weight	638900.0 kDa
排除体积 excluded_volume	797060 Å³
包络体积 envelope_volume	1061500 Å³
水化壳体积 shell_volume	139870 Å³
包络直径 envelope_diameter	196.1 Å
壳层 Rg shell_rg	69.55 Å
包络 Rg envelope_rg	57.89 Å
形状 Rg shape_rg	58.48 Å
总 Rg total_rg	58.47 Å
总原子数 total_atoms	44620
残基数 n_residues	5736
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	187.9 Å
Rg (实空间) rg_real	58.41 Å
Rg 误差 (实空间) rg_real_error	1.39 Å
I(0) (实空间) i0_real	5.7660e+09
I(0) 误差 (实空间) i0_real_error	1.1280e+08
Rg (倒空间) rg_reciprocal	59.07 Å
I(0) (倒空间) i0_reciprocal	5772000000.0000
解质量估计 total_estimate	0.8803
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	83.5 Å
偏度 Skewness skewness	0.033
峰度 Kurtosis kurtosis	-0.557
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	884800000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.845

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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	Methyltransferase 1
分子量 formula_weight	50846.8 kDa
EC 编号 ec_number	2.1.1.90
来源方法 src_method	nat
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K,M,O
原子数 atom_count	45566

MAAKRYTSMAYANADEMTFGVSKYPVKAGLDLEIGAGYTIPEINYAPRPEAGASKEKLIKEYERITTDVMERMVQVGFPAIILETEHVQQMSNNPSWGAEVAHAQKTIMEKYHDEYGIKCALRHTIGDIRENREFLQLRGDKYSVFLEAFEQCAENGADLLSVESMGGKEVFDYAVLRNDIPGLLYSIGCLGSIDMELIWTDISKIAKKTGTISAGDTDCAQANTAMFIGGGLLNKNLAHTIAVIARAISAPRSLVAYEAGAVGPGKDCGYENIIVKAITGMPMTMEGKTSTCAHSDVMGNLVMQCCDCWSNESVEYHGEFGGTTVQCWSETLAYDCALMNTALETKNDKVLRDLMMLSDRYRDPQAYMLAYDNAYRVGQSIVKDGDNIYLRAKNAAIECCNIIEEGAAGKLELSRFETKALADAKAALEALPDDMDKFMDDCLTKYKSEVKVFKPENYGF

Entity 2 polymer

描述 description	Methyltransferase 1
分子量 formula_weight	27882.9 kDa
EC 编号 ec_number	2.1.1.90
来源方法 src_method	nat
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,J,L,N,P

MLDFTEASLKKVLTRYNVALEKALTPEEAAEELYPKDELIYPIAKAIFEGEEDDVVEGLQAAIEAGKDPIDLIDDALMVGMGVVIRLYDEGVIFLPNVMMSADAMLEGIEYCKENSGATPKTKGTVVCHVAEGDVHDIGKNIVTALLRANGYNVVDLGRDVPAEEVLAAVQKEKPIMLTGTALMTTTMYAFKEVNDMLLENGIKIPFACGGGAVNQDFVSQFALGVYGEEAADAPKIADAIIAGTTDVTELREKFHKH

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	12

Entity 4 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	8

Entity 5 non-polymer

描述 description	5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE
分子量 formula_weight	1321.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	946

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6. 折叠分类 (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

结构域编号 domain_id	2i2xB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Methionine synthase domain

结构域编号 domain_id	2i2xB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	280 — Cobalamin-binding domain

结构域编号 domain_id	2i2xD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Methionine synthase domain

结构域编号 domain_id	2i2xD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	280 — Cobalamin-binding domain

结构域编号 domain_id	2i2xF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Methionine synthase domain

结构域编号 domain_id	2i2xF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	280 — Cobalamin-binding domain

结构域编号 domain_id	2i2xH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Methionine synthase domain

结构域编号 domain_id	2i2xH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	280 — Cobalamin-binding domain

结构域编号 domain_id	2i2xJ01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Methionine synthase domain

结构域编号 domain_id	2i2xJ02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	280 — Cobalamin-binding domain

结构域编号 domain_id	2i2xL01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Methionine synthase domain

结构域编号 domain_id	2i2xL02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	280 — Cobalamin-binding domain

结构域编号 domain_id	2i2xN01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Methionine synthase domain

结构域编号 domain_id	2i2xN02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	280 — Cobalamin-binding domain

结构域编号 domain_id	2i2xP01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Methionine synthase domain

结构域编号 domain_id	2i2xP02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	280 — Cobalamin-binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	101.750 Å
晶胞边长 b length_b	172.850 Å
晶胞边长 c length_c	190.540 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.86 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1843
R_work r_work	0.1818
R_free r_free	0.2315

fit	/app/data/saxs_computation/i2/2i2x/2i2x.fit
pddf	/app/data/pr_computation/i2/2i2x/2i2x.pr.out
profile	/app/data/saxs_computation/i2/2i2x/2i2x.dat

Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)