SAXSdb — 1h2a

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h2a
沉积日期 deposition_date	1997-10-17
结构标题 title	SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS
关键词 keywords	NI-FE HYDROGENASE, SO LIGAND, HYDROGEN METABOLISM, MG CENTER, MIR, MAD, 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	25.95 Å
回转半径 Rg (电子) rg_electron	24.96 Å
零角强度 I(0) i0	129042000.00
分子量 molecular_weight	89114.0 kDa
排除体积 excluded_volume	110950 Å³
包络体积 envelope_volume	125530 Å³
水化壳体积 shell_volume	39234 Å³
包络直径 envelope_diameter	84.3 Å
壳层 Rg shell_rg	34.42 Å
包络 Rg envelope_rg	25.20 Å
形状 Rg shape_rg	24.98 Å
总 Rg total_rg	25.75 Å
总原子数 total_atoms	6226
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	78.5 Å
Rg (实空间) rg_real	25.79 Å
Rg 误差 (实空间) rg_real_error	0.12 Å
I(0) (实空间) i0_real	1.2470e+08
I(0) 误差 (实空间) i0_real_error	1.2880e+06
Rg (倒空间) rg_reciprocal	25.83 Å
I(0) (倒空间) i0_reciprocal	129000000.0000
解质量估计 total_estimate	0.7211
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.2 Å
偏度 Skewness skewness	0.125
峰度 Kurtosis kurtosis	-0.463
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	7.0140
最高正则化参数 α highest_alpha	29010000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 0.917; Sysdev: 0.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.880

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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	HYDROGENASE
分子量 formula_weight	34148.0 kDa
EC 编号 ec_number	1.18.99.1
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	6864

MKISIGLGKEGVEERLAERGVSRRDFLKFCTAIAVTMGMGPAFAPEVARALMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGEFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIGCSEPDFWDAMTPFYQN

Entity 2 polymer

描述 description	HYDROGENASE
分子量 formula_weight	62711.4 kDa
EC 编号 ec_number	1.18.99.1
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

MSGCRAQNAPGGIPVTPKSSYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRDPRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQYLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKAVQDKLKTFVETGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFVDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVVFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDRYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQAEGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNNVSPVEASLIGTPVADAKRPVEILRTVHSFDPCIACGVHVIDGHTNEVHKFRIL

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	NI-FE ACTIVE CENTER
分子量 formula_weight	251.7 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	638

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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	d1h2al_
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	d1h2as_
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	1h2aL00
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	1h2aS01
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	1h2aS02
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 (3)

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晶胞边长 a length_a	101.500 Å
晶胞边长 b length_b	126.500 Å
晶胞边长 c length_c	66.510 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	1.800 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2780

fit	/app/data/saxs_computation/h2/1h2a/1h2a.fit
pddf	/app/data/pr_computation/h2/1h2a/1h2a.pr.out
profile	/app/data/saxs_computation/h2/1h2a/1h2a.dat

SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS

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 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)