1yqw

Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

Method: X-RAY DIFFRACTION D_max: 144.6 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	1yqw
沉积日期 deposition_date	2005-02-02
结构标题 title	Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase
关键词 keywords	NI-FE HYDROGENASE UNREADY STATE, 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	44.16 Å
回转半径 Rg (电子) rg_electron	43.88 Å
零角强度 I(0) i0	1058670000.00
分子量 molecular_weight	266950.0 kDa
排除体积 excluded_volume	332330 Å³
包络体积 envelope_volume	397720 Å³
水化壳体积 shell_volume	73915 Å³
包络直径 envelope_diameter	147.0 Å
壳层 Rg shell_rg	49.79 Å
包络 Rg envelope_rg	43.60 Å
形状 Rg shape_rg	43.86 Å
总 Rg total_rg	44.19 Å
总原子数 total_atoms	18605
残基数 n_residues	2417
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	144.6 Å
Rg (实空间) rg_real	44.09 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	1.0590e+09
I(0) 误差 (实空间) i0_real_error	1.9080e+07
Rg (倒空间) rg_reciprocal	44.16 Å
I(0) (倒空间) i0_reciprocal	1059000000.0000
解质量估计 total_estimate	0.8905
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	44.2 Å
偏度 Skewness skewness	0.183
峰度 Kurtosis kurtosis	-0.706
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	425000000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.914

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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 (12)

Entity 1 polymer

描述 description	Periplasmic [NiFe] hydrogenase small subunit
分子量 formula_weight	28347.3 kDa
EC 编号 ec_number	1.12.2.1
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	20497

LTAKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG

Entity 2 polymer

描述 description	Periplasmic [NiFe] hydrogenase large subunit
分子量 formula_weight	59713.3 kDa
EC 编号 ec_number	1.12.2.1
突变 mutation	S499A
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	Q,R,S

MAESKPTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVNLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPSKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPATWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH

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	6

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	3

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	17

Entity 6 non-polymer

描述 description	NICKEL (II) ION
分子量 formula_weight	58.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 7 non-polymer

描述 description	FE (II) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 8 non-polymer

描述 description	BICARBONATE ION
分子量 formula_weight	61.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 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	3

Entity 10 non-polymer

描述 description	CARBONMONOXIDE-(DICYANO) IRON
分子量 formula_weight	135.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 11 non-polymer

描述 description	PEROXIDE ION
分子量 formula_weight	32.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 12 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	1848

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1yqwa_
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

结构域编号 domain_id	d1yqwb_
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

结构域编号 domain_id	d1yqwc_
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

结构域编号 domain_id	d1yqwq_
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	d1yqwr_
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	d1yqws_
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

CATH v4.4 (9 domains)

结构域编号 domain_id	1yqwA01
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	1yqwA02
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

结构域编号 domain_id	1yqwB01
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	1yqwB02
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

结构域编号 domain_id	1yqwC01
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	1yqwC02
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

结构域编号 domain_id	1yqwQ00
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	1yqwR00
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	1yqwS00
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

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7. 引用文献 (3)

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晶胞边长 a length_a	64.410 Å
晶胞边长 b length_b	99.700 Å
晶胞边长 c length_c	182.830 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.42 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	1.830 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1482
R_work r_work	0.1463
R_free r_free	0.1847

fit	/app/data/saxs_computation/yq/1yqw/1yqw.fit
pddf	/app/data/pr_computation/yq/1yqw/1yqw.pr.out
profile	/app/data/saxs_computation/yq/1yqw/1yqw.dat

Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

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 (12)

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 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 water

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)