2d0p

Structure of diol dehydratase-reactivating factor in nucleotide free form

Method: X-RAY DIFFRACTION D_max: 120.7 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	2d0p
沉积日期 deposition_date	2005-08-05
结构标题 title	Structure of diol dehydratase-reactivating factor in nucleotide free form
关键词 keywords	CHAPERONE; CHAPERONE
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	37.31 Å
回转半径 Rg (电子) rg_electron	36.57 Å
零角强度 I(0) i0	347353000.00
分子量 molecular_weight	151770.0 kDa
排除体积 excluded_volume	190690 Å³
包络体积 envelope_volume	246660 Å³
水化壳体积 shell_volume	55921 Å³
包络直径 envelope_diameter	128.3 Å
壳层 Rg shell_rg	43.27 Å
包络 Rg envelope_rg	35.98 Å
形状 Rg shape_rg	36.58 Å
总 Rg total_rg	36.97 Å
总原子数 total_atoms	10656
残基数 n_residues	1430
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	120.7 Å
Rg (实空间) rg_real	37.12 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	3.4740e+08
I(0) 误差 (实空间) i0_real_error	6.6090e+06
Rg (倒空间) rg_reciprocal	37.24 Å
I(0) (倒空间) i0_reciprocal	347400000.0000
解质量估计 total_estimate	0.8917
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	48.9 Å
偏度 Skewness skewness	0.150
峰度 Kurtosis kurtosis	-0.421
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35860000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.942

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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 (5)

Entity 1 polymer

描述 description	diol dehydratase-reactivating factor large subunit
分子量 formula_weight	64329.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	10689

MRYIAGIDIGNSSTEVALATLDEAGALTITHSALAETTGIKGTLRNVFGIQEALALVARGAGIAVSDISLIRINEATPVIGDVAMETITETIITESTMIGHNPKTPGGAGLGTGITITPQELLTRPADAPYILVVSSAFDFADIASVINASLRAGYQITGVILQRDDGVLVSNRLEKPLPIVDEVLYIDRIPLGMLAAIEVAVPGKVIETLSNPYGIATVFNLSPEETKNIVPMARALIGNRSAVVVKTPSGDVKARAIPAGNLELLAQGRSVRVDVAAGAEAIMKAVDGCGRLDNVTGESGTNIGGMLEHVRQTMAELTNKPSSEIFIQDLLAVDTSVPVSVTGGLAGEFSLEQAVGIASMVKSDRLQMAMIAREIEQKLNIDVQIGGAEAEAAILGALTTPGTTRPLAILDLGAGSTDASIINPKGDIIATHLAGAGDMVTMIIARELGLEDRYLAEEIKKYPLAKVESLFHLRHEDGSVQFFSTPLPPAVFARVCVVKADELVPLPGDLALEKVRAIRRSAKERVFVTNALRALRQVSPTGNIRDIPFVVLVGGSSLDFEVPQLVTDALAHYRLVAGRGNIRGSEGPRNAVATGLILSWHKEFAHER

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI 分类编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	diol dehydratase-reactivating factor small subunit
分子量 formula_weight	13637.3 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

MNGNHSAPAIAIAVIDGCDGLWREVLLGIEEEGIPFRLQHHPAGEVVDSAWQAARSSPLLVGIACDRHMLVVHYKNLPASAPLFTLMHHQDSQAHRNTGNNAARLVKGIPFRDLNSEATGEQQDE

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI 分类编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	33

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2d0pa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.6 — Swiveling domain of dehydratase reactivase alpha subunit
家族 Family family	c.8.6.1 — Swiveling domain of dehydratase reactivase alpha subunit

结构域编号 domain_id	d2d0pa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.6 — ATPase domain of dehydratase reactivase alpha subunit

结构域编号 domain_id	d2d0pa3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.6 — ATPase domain of dehydratase reactivase alpha subunit

结构域编号 domain_id	d2d0pb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
家族 Family family	c.51.3.2 — Dehydratase-reactivating factor beta subunit

结构域编号 domain_id	d2d0pc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.6 — Swiveling domain of dehydratase reactivase alpha subunit
家族 Family family	c.8.6.1 — Swiveling domain of dehydratase reactivase alpha subunit

结构域编号 domain_id	d2d0pc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.6 — ATPase domain of dehydratase reactivase alpha subunit

结构域编号 domain_id	d2d0pc3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.6 — ATPase domain of dehydratase reactivase alpha subunit

结构域编号 domain_id	d2d0pd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
家族 Family family	c.51.3.2 — Dehydratase-reactivating factor beta subunit

CATH v4.4 (12 domains)

结构域编号 domain_id	2d0pA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	2d0pA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	470 — Ribosomal Protein L22; Chain A
同源超家族 H-superfamily homologous superfamily	30 — Coenzyme B12-Dependent Enzyme linker domain

结构域编号 domain_id	2d0pA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	30 — Glucose Oxidase; domain 1
同源超家族 H-superfamily homologous superfamily	70 — Swiveling domain of dehydratase reactivase alpha subunit

结构域编号 domain_id	2d0pA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	2d0pA05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	2d0pB00
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	10150 — B12-dependent dehydatase associated subunit

结构域编号 domain_id	2d0pC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	2d0pC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	470 — Ribosomal Protein L22; Chain A
同源超家族 H-superfamily homologous superfamily	30 — Coenzyme B12-Dependent Enzyme linker domain

结构域编号 domain_id	2d0pC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	30 — Glucose Oxidase; domain 1
同源超家族 H-superfamily homologous superfamily	70 — Swiveling domain of dehydratase reactivase alpha subunit

结构域编号 domain_id	2d0pC04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	2d0pC05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	2d0pD00
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	10150 — B12-dependent dehydatase associated subunit

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7. 引用文献 (1)

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晶胞边长 a length_a	81.920 Å
晶胞边长 b length_b	85.370 Å
晶胞边长 c length_c	296.990 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	40.580 Å
R 因子 r_factor	0.2380
R_work r_work	0.2380
R_free r_free	0.3130

fit	/app/data/saxs_computation/d0/2d0p/2d0p.fit
pddf	/app/data/pr_computation/d0/2d0p/2d0p.pr.out
profile	/app/data/saxs_computation/d0/2d0p/2d0p.dat

Structure of diol dehydratase-reactivating factor in nucleotide free form

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)