SAXSdb — 1ubt

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ubt
沉积日期 deposition_date	2003-04-04
结构标题 title	Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F
关键词 keywords	High resolution crystal structure, [NiFe]hydrogenase, Oxidoreductase, Carbon Monoxide Complex; 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	25.64 Å
回转半径 Rg (电子) rg_electron	24.64 Å
零角强度 I(0) i0	128277000.00
分子量 molecular_weight	89107.0 kDa
排除体积 excluded_volume	111020 Å³
包络体积 envelope_volume	121980 Å³
水化壳体积 shell_volume	38525 Å³
包络直径 envelope_diameter	85.2 Å
壳层 Rg shell_rg	34.10 Å
包络 Rg envelope_rg	24.96 Å
形状 Rg shape_rg	24.67 Å
总 Rg total_rg	25.44 Å
总原子数 total_atoms	6228
残基数 n_residues	801
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	83.3 Å
Rg (实空间) rg_real	25.46 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	1.2830e+08
I(0) 误差 (实空间) i0_real_error	1.5080e+06
Rg (倒空间) rg_reciprocal	25.52 Å
I(0) (倒空间) i0_reciprocal	128300000.0000
解质量估计 total_estimate	0.8828
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	32.3 Å
偏度 Skewness skewness	0.108
峰度 Kurtosis kurtosis	-0.501
角度范围 angular_range	— – 0.3100 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	30130000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.997

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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 (7)

Entity 1 polymer

描述 description	Periplasmic [NiFe] hydrogenase Small subunit
分子量 formula_weight	28789.7 kDa
EC 编号 ec_number	1.12.2.1
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	S
原子数 atom_count	7233

LMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGEFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIGCSEPDFWDAMTPFYQN

Entity 2 polymer

描述 description	Periplasmic [NiFe] hydrogenase Large subunit
分子量 formula_weight	59208.4 kDa
EC 编号 ec_number	1.12.2.1
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L

SSYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRDPRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQYLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKAVQDKLKTFVETGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFVDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVVFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDRYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQAEGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPVEASLIGTPVADAKRPVEILRTVHSFDPCIACGVH

Entity 3 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	FE3-S4 CLUSTER
分子量 formula_weight	295.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	1

Entity 6 non-polymer

描述 description	(MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)
分子量 formula_weight	230.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	1005

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6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ubtl_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.18 — HydB/Nqo4-like
超家族 Superfamily superfamily	e.18.1 — HydB/Nqo4-like
家族 Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

结构域编号 domain_id	d1ubts_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.19 — HydA/Nqo6-like
超家族 Superfamily superfamily	e.19.1 — HydA/Nqo6-like
家族 Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

CATH v4.4 (3 domains)

结构域编号 domain_id	1ubtL00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

结构域编号 domain_id	1ubtS01
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	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

结构域编号 domain_id	1ubtS02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	98.030 Å
晶胞边长 b length_b	126.010 Å
晶胞边长 c length_c	66.570 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.340 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1264
R_work r_work	0.1232
R_free r_free	0.1788

fit	/app/data/saxs_computation/ub/1ubt/1ubt.fit
pddf	/app/data/pr_computation/ub/1ubt/1ubt.pr.out
profile	/app/data/saxs_computation/ub/1ubt/1ubt.dat

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

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

衍射实验 Diffraction

5. 实体与聚合体信息 (7)

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 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)