1u6j

The Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.4A resolution

Method: X-RAY DIFFRACTION D_max: 180.6 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	1u6j
沉积日期 deposition_date	2004-07-30
结构标题 title	The Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.4A resolution
关键词 keywords	MONOMER: ALPHA/BETA DOMAIN, HELIX BUNDLE; TRIMER OF DIMERS, OXIDOREDUCTASE; OXIDOREDUCTASE
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	53.90 Å
回转半径 Rg (电子) rg_electron	53.77 Å
零角强度 I(0) i0	2042590000.00
分子量 molecular_weight	374850.0 kDa
排除体积 excluded_volume	467130 Å³
包络体积 envelope_volume	589010 Å³
水化壳体积 shell_volume	90788 Å³
包络直径 envelope_diameter	176.2 Å
壳层 Rg shell_rg	56.71 Å
包络 Rg envelope_rg	52.99 Å
形状 Rg shape_rg	53.79 Å
总 Rg total_rg	53.75 Å
总原子数 total_atoms	26192
残基数 n_residues	3384
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	180.6 Å
Rg (实空间) rg_real	54.00 Å
Rg 误差 (实空间) rg_real_error	1.84 Å
I(0) (实空间) i0_real	2.0430e+09
I(0) 误差 (实空间) i0_real_error	4.3530e+07
Rg (倒空间) rg_reciprocal	53.79 Å
I(0) (倒空间) i0_reciprocal	2042000000.0000
解质量估计 total_estimate	0.8692
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	49.8 Å
偏度 Skewness skewness	0.310
峰度 Kurtosis kurtosis	-0.704
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	495300000.0000
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: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.756

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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	F420-dependent methylenetetrahydromethanopterin dehydrogenase
分子量 formula_weight	31415.9 kDa
EC 编号 ec_number	1.5.99.9
来源方法 src_method	man
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	26753

MTVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEAAVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPGLKVKDEMEEQGLGYILVKPDAMLGARREFLDPVEMAIYNADLMKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFMEDPE

来源 Source

来源生物 organism	Methanopyrus kandleri
NCBI 分类编号 ncbi_taxonomy_id	2320
宿主生物 host_organism	Escherichia coli BL21

Entity 2 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	8

Entity 3 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	561

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1u6ja_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6je_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6ji_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jj_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jk_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d1u6jl_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

CATH v4.4 (24 domains)

结构域编号 domain_id	1u6jA01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jA02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jB01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jB02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jC01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jC02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jD01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jD02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jE01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jE02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jF01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jF02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jG01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jG02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jH01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jH02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jI01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jI02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jJ01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jJ02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jK01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jK02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1u6jL01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	1u6jL02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	120 —

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7. 引用文献 (2)

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晶胞边长 a length_a	150.900 Å
晶胞边长 b length_b	118.900 Å
晶胞边长 c length_c	219.200 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.01 °
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	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1750
R_free r_free	0.2350

fit	/app/data/saxs_computation/u6/1u6j/1u6j.fit
pddf	/app/data/pr_computation/u6/1u6j/1u6j.pr.out
profile	/app/data/saxs_computation/u6/1u6j/1u6j.dat