1hfe

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

Method: X-RAY DIFFRACTION D_max: 106.9 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	1hfe
沉积日期 deposition_date	1998-11-11
结构标题 title	1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS
关键词 keywords	FE-ONLY HYDROGENASE, HYDROGENE METABOLISM, PERIPLASM, HYDROGENASE; HYDROGENASE
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	33.14 Å
回转半径 Rg (电子) rg_electron	32.60 Å
零角强度 I(0) i0	197212000.00
分子量 molecular_weight	109530.0 kDa
排除体积 excluded_volume	135340 Å³
包络体积 envelope_volume	161380 Å³
水化壳体积 shell_volume	41184 Å³
包络直径 envelope_diameter	110.1 Å
壳层 Rg shell_rg	39.54 Å
包络 Rg envelope_rg	32.59 Å
形状 Rg shape_rg	32.56 Å
总 Rg total_rg	33.22 Å
总原子数 total_atoms	7549
残基数 n_residues	970
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	106.9 Å
Rg (实空间) rg_real	33.27 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	1.9720e+08
I(0) 误差 (实空间) i0_real_error	3.4370e+06
Rg (倒空间) rg_reciprocal	33.22 Å
I(0) (倒空间) i0_reciprocal	197200000.0000
解质量估计 total_estimate	0.8732
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	28.9 Å
偏度 Skewness skewness	0.341
峰度 Kurtosis kurtosis	-0.693
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	135800000.0000
实空间数据点数 n_real_points	49
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: 0.903; Smooth: 0.888

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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 (10)

Entity 1 polymer

描述 description	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))
分子量 formula_weight	13646.8 kDa
EC 编号 ec_number	1.18.99.1
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	S,T
原子数 atom_count	9079

MQIASITRRGFLKVACVTTGAALIGIRMTGKAVAAVKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE

Entity 2 polymer

描述 description	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))
分子量 formula_weight	46011.1 kDa
EC 编号 ec_number	1.18.99.1
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MSRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEAMDRTTTRLYAGLKKRLAMASANKA

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	1

Entity 4 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	4

Entity 5 non-polymer

描述 description	CYANIDE ION
分子量 formula_weight	26.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 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 7 non-polymer

描述 description	1,3-PROPANEDITHIOL
分子量 formula_weight	108.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 non-polymer

描述 description	CARBON MONOXIDE
分子量 formula_weight	28.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 9 non-polymer

描述 description	CYSTEINE
分子量 formula_weight	121.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 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	1179

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1hfel1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.96 — Fe-only hydrogenase
超家族 Superfamily superfamily	c.96.1 — Fe-only hydrogenase
家族 Family family	c.96.1.1 — Fe-only hydrogenase

结构域编号 domain_id	d1hfel2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
家族 Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

结构域编号 domain_id	d1hfem1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.96 — Fe-only hydrogenase
超家族 Superfamily superfamily	c.96.1 — Fe-only hydrogenase
家族 Family family	c.96.1.1 — Fe-only hydrogenase

结构域编号 domain_id	d1hfem2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
家族 Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

结构域编号 domain_id	d1hfes_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
超家族 Superfamily superfamily	a.137.4 — Fe-only hydrogenase smaller subunit
家族 Family family	a.137.4.1 — Fe-only hydrogenase smaller subunit

结构域编号 domain_id	d1hfet_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
超家族 Superfamily superfamily	a.137.4 — Fe-only hydrogenase smaller subunit
家族 Family family	a.137.4.1 — Fe-only hydrogenase smaller subunit

CATH v4.4 (8 domains)

结构域编号 domain_id	1hfeL01
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	1780 —

结构域编号 domain_id	1hfeL02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1hfeL03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	950 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3

结构域编号 domain_id	1hfeM01
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	1780 —

结构域编号 domain_id	1hfeM02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1hfeM03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	950 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3

结构域编号 domain_id	1hfeS00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	260 — G Protein Gi Gamma 2
同源超家族 H-superfamily homologous superfamily	20 — Iron hydrogenase, small subunit

结构域编号 domain_id	1hfeT00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	260 — G Protein Gi Gamma 2
同源超家族 H-superfamily homologous superfamily	20 — Iron hydrogenase, small subunit

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7. 引用文献 (1)

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晶胞边长 a length_a	128.970 Å
晶胞边长 b length_b	123.070 Å
晶胞边长 c length_c	65.070 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	7.000 Å
R 因子 r_factor	—
R_work r_work	0.1582
R_free r_free	0.1820

fit	/app/data/saxs_computation/hf/1hfe/1hfe.fit
pddf	/app/data/pr_computation/hf/1hfe/1hfe.pr.out
profile	/app/data/saxs_computation/hf/1hfe/1hfe.dat

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

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 (10)

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 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)