1t1r

Crystal Structure of the Reductoisomerase Complexed with a Bisphosphonate

Method: X-RAY DIFFRACTION D_max: 99.4 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1t1r
沉积日期 deposition_date	2004-04-17
结构标题 title	Crystal Structure of the Reductoisomerase Complexed with a Bisphosphonate
关键词 keywords	three domains, oxidoreductase; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	30.80 Å
回转半径 Rg (电子) rg_electron	30.23 Å
零角强度 I(0) i0	128086000.00
分子量 molecular_weight	87442.0 kDa
排除体积 excluded_volume	108540 Å³
包络体积 envelope_volume	130720 Å³
水化壳体积 shell_volume	36677 Å³
包络直径 envelope_diameter	107.7 Å
壳层 Rg shell_rg	36.73 Å
包络 Rg envelope_rg	30.65 Å
形状 Rg shape_rg	30.17 Å
总 Rg total_rg	30.97 Å
总原子数 total_atoms	6102
残基数 n_residues	796
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	99.4 Å
Rg (实空间) rg_real	30.87 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	1.2810e+08
I(0) 误差 (实空间) i0_real_error	2.0200e+06
Rg (倒空间) rg_reciprocal	30.85 Å
I(0) (倒空间) i0_reciprocal	128100000.0000
解质量估计 total_estimate	0.8844
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	33.1 Å
偏度 Skewness skewness	0.398
峰度 Kurtosis kurtosis	-0.413
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21420000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.839

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	1-deoxy-D-xylulose 5-phosphate reductoisomerase
分子量 formula_weight	43357.7 kDa
EC 编号 ec_number	1.1.1.267
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,B
原子数 atom_count	6192

GKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRMVEQCLEFSPRYAVMDDEASAKLLKTMLQQQGSRTEVLSGQQAACDMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFMDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATMTPDQACRHPNWSMGRKISVDSATMMNKGLEYIEARWLFNASASQMEVLIHPQSVIHSMVRYQDGSVLAQLGEPDMRTPIAHTMAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKMDMREPQCVDDVLSVDANAREVARKEVMRLAS

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 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	2

Entity 3 non-polymer

描述 description	[(ISOQUINOLIN-1-YLAMINO)-PHOSPHONO-METHYL]-PHOSPHONIC ACID
分子量 formula_weight	318.2 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	90

▼

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1t1ra1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.69 — Left-handed superhelix
超家族 Superfamily superfamily	a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
家族 Family family	a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain

结构域编号 domain_id	d1t1ra2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1t1ra3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1t1ra4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

结构域编号 domain_id	d1t1ra5
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1t1rb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.69 — Left-handed superhelix
超家族 Superfamily superfamily	a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
家族 Family family	a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain

结构域编号 domain_id	d1t1rb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1t1rb3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1t1rb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

结构域编号 domain_id	d1t1rb5
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

结构域编号 domain_id	1t1rA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1t1rA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

结构域编号 domain_id	1t1rB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1t1rB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	182.381 Å
晶胞边长 b length_b	59.042 Å
晶胞边长 c length_c	86.978 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	2.300 Å
最低分辨率 resolution_low	45.000 Å
R 因子 r_factor	—
R_work r_work	0.2180
R_free r_free	0.2700

fit	/app/data/saxs_computation/t1/1t1r/1t1r.fit
pddf	/app/data/pr_computation/t1/1t1r/1t1r.pr.out
profile	/app/data/saxs_computation/t1/1t1r/1t1r.dat