2hyb

Crystal Structure of Hexameric DsrEFH

Method: X-RAY DIFFRACTION D_max: 156.8 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	2hyb
沉积日期 deposition_date	2006-08-04
结构标题 title	Crystal Structure of Hexameric DsrEFH
关键词 keywords	;DsrE, DsrF, DsrH, Sulfur, Structural Genomics, PSI, Protein Structure Initiative, Berkeley Structural Genomics Center, BSGC, TRANSFERASE ;; TRANSFERASE
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	49.79 Å
回转半径 Rg (电子) rg_electron	49.39 Å
零角强度 I(0) i0	858156000.00
分子量 molecular_weight	243740.0 kDa
排除体积 excluded_volume	304340 Å³
包络体积 envelope_volume	394370 Å³
水化壳体积 shell_volume	65642 Å³
包络直径 envelope_diameter	158.5 Å
壳层 Rg shell_rg	54.00 Å
包络 Rg envelope_rg	48.40 Å
形状 Rg shape_rg	49.38 Å
总 Rg total_rg	49.57 Å
总原子数 total_atoms	17193
残基数 n_residues	2178
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	156.8 Å
Rg (实空间) rg_real	49.70 Å
Rg 误差 (实空间) rg_real_error	1.28 Å
I(0) (实空间) i0_real	8.5820e+08
I(0) 误差 (实空间) i0_real_error	1.5940e+07
Rg (倒空间) rg_reciprocal	49.79 Å
I(0) (倒空间) i0_reciprocal	858200000.0000
解质量估计 total_estimate	0.8522
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	78.4 Å
偏度 Skewness skewness	0.072
峰度 Kurtosis kurtosis	-0.924
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	513100000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.784

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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 (4)

Entity 1 polymer

描述 description	Putative sulfurtransferase dsrE
分子量 formula_weight	14607.3 kDa
EC 编号 ec_number	2.8.1.-
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,G,J,M,P
原子数 atom_count	17611

MKFALQINEGPYQHQASDSAYQFAKAALEKGHEIFRVFFYHDGVNNSTRLTTPPQDDRHIVNRWAELAEQYELDMVVCVAAAQRRGIVDEGEASRNGKDATNIHPKFRISGLGQLVEAAIQADRLVVFGD

来源 Source

来源生物 organism	Allochromatium vinosum
NCBI 分类编号 ncbi_taxonomy_id	1049
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Intracellular sulfur oxidation protein dsrF
分子量 formula_weight	15606.4 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E,H,K,N,Q

MSEVVKKFMYLNRKAPYGTIYAWEALEVVLIGAAFDQDVCVLFLDDGVYQLTRGQDTKGIGMKNFSPTYRTLGDYEVRRIYVDRDSLEARGLTQDDLVEIAFEDMETEEEFDNIVEVIDSARVSELMNESDAVFSF

来源 Source

来源生物 organism	Allochromatium vinosum
NCBI 分类编号 ncbi_taxonomy_id	1049
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

描述 description	DsrH
分子量 formula_weight	11094.6 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F,I,L,O,R

MSILHTVNKSPFERNSLESCLKFATEGASVLLFEDGIYAALAGTRVESQVTEALGKLKLYVLGPDLKARGFSDERVIPGISVVDYAGFVDLTTECDTVQAWL

来源 Source

来源生物 organism	Allochromatium vinosum
NCBI 分类编号 ncbi_taxonomy_id	1049
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 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	418

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d2hyba_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

结构域编号 domain_id	d2hybd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybe_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

结构域编号 domain_id	d2hybg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybi_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

结构域编号 domain_id	d2hybj_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybk_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybl_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

结构域编号 domain_id	d2hybm_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybn_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybo_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

结构域编号 domain_id	d2hybp_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybq_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2hybr_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

CATH v4.4 (18 domains)

结构域编号 domain_id	2hybA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybM00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybN00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybO00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybP00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybQ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2hybR00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

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7. 引用文献 (1)

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晶胞边长 a length_a	56.610 Å
晶胞边长 b length_b	183.110 Å
晶胞边长 c length_c	107.830 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.57 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	2.500 Å
最低分辨率 resolution_low	19.980 Å
R 因子 r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2620

Crystal Structure of Hexameric DsrEFH

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 water

6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

CATH v4.4 (18 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/hy/2hyb/2hyb.fit
pddf	/app/data/pr_computation/hy/2hyb/2hyb.pr.out
profile	/app/data/saxs_computation/hy/2hyb/2hyb.dat