1nbw

Glycerol dehydratase reactivase

Method: X-RAY DIFFRACTION D_max: 121.4 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	1nbw
沉积日期 deposition_date	2002-12-04
结构标题 title	Glycerol dehydratase reactivase
关键词 keywords	Glycerol dehydratase, Reactivase, Molecular chaperone, Actin-like ATPase domain, beta/beta/alpha swiveling domain, HYDROLASE; HYDROLASE
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	37.47 Å
回转半径 Rg (电子) rg_electron	36.64 Å
零角强度 I(0) i0	340282000.00
分子量 molecular_weight	149890.0 kDa
排除体积 excluded_volume	188140 Å³
包络体积 envelope_volume	246600 Å³
水化壳体积 shell_volume	55597 Å³
包络直径 envelope_diameter	130.3 Å
壳层 Rg shell_rg	43.41 Å
包络 Rg envelope_rg	36.26 Å
形状 Rg shape_rg	36.67 Å
总 Rg total_rg	37.00 Å
总原子数 total_atoms	10520
残基数 n_residues	1436
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	121.4 Å
Rg (实空间) rg_real	37.28 Å
Rg 误差 (实空间) rg_real_error	1.32 Å
I(0) (实空间) i0_real	3.4030e+08
I(0) 误差 (实空间) i0_real_error	6.2240e+06
Rg (倒空间) rg_reciprocal	37.40 Å
I(0) (倒空间) i0_reciprocal	340300000.0000
解质量估计 total_estimate	0.8907
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	46.3 Å
偏度 Skewness skewness	0.147
峰度 Kurtosis kurtosis	-0.423
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	31680000.0000
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: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.944

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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	GLYCEROL DEHYDRATASE REACTIVASE ALPHA SUBUNIT
分子量 formula_weight	63650.2 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	11079

MPLIAGIDIGNATTEVALASDYPQARAFVASGIVATTGMKGTRDNIAGTLAALEQALAKTPWSMSDVSRIYLNEAAPVIGDVAMETITETIITESTMIGHNPQTPGGVGVGVGTTIALGRLATLPAAQYAEGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDDGVLVNNRLRKTLPVVDEVTLLEQVPEGVMAAVEVAAPGQVVRILSNPYGIATFFGLSPEETQAIVPIARALIGNRSAVVLKTPQGDVQSRVIPAGNLYISGEKRRGEADVAEGAEAIMQAMSACAPVRDIRGEPGTHAGGMLERVRKVMASLTGHEMSAIYIQDLLAVDTFIPRKVQGGMAGECAMENAVGMAAMVKADRLQMQVIARELSARLQTEVVVGGVEANMAIAGALTTPGCAAPLAILDLGAGSTDAAIVNAEGQITAVHLAGAGNMVSLLIKTELGLEDLSLAEAIKKYPLAKVESLFSIRHENGAVEFFREALSPAVFAKVVYIKEGELVPIDNASPLEKIRLVRRQAKEKVFVTNCLRALRQVSPGGSIRDIAFVVLVGGSSLDFEIPQLITEALSHYGVVAGQGNIRGTEGPRNAVATGLLLAGQAN

来源 Source

来源生物 organism	Klebsiella pneumoniae
NCBI 分类编号 ncbi_taxonomy_id	573
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	GLYCEROL DEHYDRATASE REACTIVASE BETA SUBUNIT
分子量 formula_weight	12005.4 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

MSLSPPGVRLFYDPRGHHAGAINELCWGLEEQGVPCQTITYDGGGDAAALGALAARSSPLRVGIGLSASGEIALTHAQLPADAPLATGHVTDSDDQLRTLGANAGQLVKVLPLSERN

来源 Source

来源生物 organism	Klebsiella pneumoniae
NCBI 分类编号 ncbi_taxonomy_id	573
宿主生物 host_organism	Escherichia coli

Entity 3 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 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	559

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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	d1nbwa1
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	d1nbwa2
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	d1nbwa3
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	d1nbwb_
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	d1nbwc1
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	d1nbwc2
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	d1nbwc3
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	d1nbwd_
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	1nbwA01
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	1nbwA02
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	1nbwA03
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	1nbwA04
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	1nbwA05
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	1nbwB00
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	1nbwC01
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	1nbwC02
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	1nbwC03
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	1nbwC04
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	1nbwC05
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	1nbwD00
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	110.000 Å
晶胞边长 b length_b	110.000 Å
晶胞边长 c length_c	332.200 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	16

空间群 space_group	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2320
R_free r_free	0.2710

fit	/app/data/saxs_computation/nb/1nbw/1nbw.fit
pddf	/app/data/pr_computation/nb/1nbw/1nbw.pr.out
profile	/app/data/saxs_computation/nb/1nbw/1nbw.dat

Glycerol dehydratase reactivase

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 non-polymer

Entity 4 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)