1l1l

CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE

Method: X-RAY DIFFRACTION D_max: 180.7 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	1l1l
沉积日期 deposition_date	2002-02-18
结构标题 title	CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE
关键词 keywords	10-stranded alpha-beta barrel, central finger loop, OXIDOREDUCTASE; OXIDOREDUCTASE
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	54.41 Å
回转半径 Rg (电子) rg_electron	54.21 Å
零角强度 I(0) i0	1453550000.00
分子量 molecular_weight	316900.0 kDa
排除体积 excluded_volume	395560 Å³
包络体积 envelope_volume	567690 Å³
水化壳体积 shell_volume	87457 Å³
包络直径 envelope_diameter	179.7 Å
壳层 Rg shell_rg	57.17 Å
包络 Rg envelope_rg	53.03 Å
形状 Rg shape_rg	54.22 Å
总 Rg total_rg	54.28 Å
总原子数 total_atoms	22352
残基数 n_residues	2868
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	180.7 Å
Rg (实空间) rg_real	54.30 Å
Rg 误差 (实空间) rg_real_error	1.97 Å
I(0) (实空间) i0_real	1.4540e+09
I(0) 误差 (实空间) i0_real_error	2.8500e+07
Rg (倒空间) rg_reciprocal	54.48 Å
I(0) (倒空间) i0_reciprocal	1454000000.0000
解质量估计 total_estimate	0.8848
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	74.8 Å
偏度 Skewness skewness	0.112
峰度 Kurtosis kurtosis	-0.719
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	137300000.0000
实空间数据点数 n_real_points	30
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: 1.000; Smooth: 0.854

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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 (2)

Entity 1 polymer

描述 description	RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE
分子量 formula_weight	82071.0 kDa
EC 编号 ec_number	1.17.4.2
突变 mutation	C731/736S
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	25227

MSEEISLSAEFIDRVKASVKPHWGKLGWVTYKRTYARWLPEKGRSENWDETVKRVVEGNINLDPRLQDSPSLELKQSLTEEAERLYKLIYGLGATPSGRNLWISGTDYQRRTGDSLNNCWFVAIRPQKYGDSKIVPSYLGKQEKAVSMPFSFLFDELMKGGGVGFSVARSNISQIPRVDFAIDLQLVVDETSESYDASVKVGAVGKNELVQDADSIYYRLPDTREGWVLANALLIDLHFAQTNPDRKQKLILDLSDIRPYGAEIHGFGGTASGPMPLISMLLDVNEVLNNKAGGRLTAVDAADICNLIGKAVVAGNVRRSAELALGSNDDQDFISMKQDQEKLMHHRWASNNSVAVDSAFSGYQPIAAGIRENGEPGIVNLDLSKNYGRIVDGYQAGIDGDVEGTNPCGEISLANGEPCNLFEVFPLIAEEQGWDLQEVFALAARYAKRVTFSPYDWEISREIIQKNRRIGISMSGIQDWLLTRLGNRVVTGFKDDFDPETHEAIKVPVYDKRAIKMVDQLYKAVVKADQDYSKTLGCNESIKHTTVKPSGTVAKLAGASEGMHFHYGAYLIQRIRFQDSDPLLPALKACGYRTEADIYTENTTCVEFPIKAVGADNPNFASAGTVSIAEQFATQAFLQTYWSDNAVSCTITFQDSEGDQVESLLRQYRFITKSTSLLPYFGGSLQQAPKEPIDKETYEKRSQEITGNVEEVFSQLNSDVKDLELVDQTDCEGGACPIK

来源 Source

来源生物 organism	Lactobacillus leichmannii
NCBI 分类编号 ncbi_taxonomy_id	28039
宿主生物 host_organism	Escherichia coli

Entity 2 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	2875

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1l1la_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.7 — PFL-like glycyl radical enzymes
超家族 Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
家族 Family family	c.7.1.4 — B12-dependent (class II) ribonucleotide reductase

结构域编号 domain_id	d1l1lb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.7 — PFL-like glycyl radical enzymes
超家族 Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
家族 Family family	c.7.1.4 — B12-dependent (class II) ribonucleotide reductase

结构域编号 domain_id	d1l1lc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.7 — PFL-like glycyl radical enzymes
超家族 Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
家族 Family family	c.7.1.4 — B12-dependent (class II) ribonucleotide reductase

结构域编号 domain_id	d1l1ld_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.7 — PFL-like glycyl radical enzymes
超家族 Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
家族 Family family	c.7.1.4 — B12-dependent (class II) ribonucleotide reductase

CATH v4.4 (12 domains)

结构域编号 domain_id	1l1lA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1l1lA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1620 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2

结构域编号 domain_id	1l1lA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1390 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3

结构域编号 domain_id	1l1lB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1l1lB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1620 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2

结构域编号 domain_id	1l1lB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1390 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3

结构域编号 domain_id	1l1lC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1l1lC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1620 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2

结构域编号 domain_id	1l1lC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1390 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3

结构域编号 domain_id	1l1lD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1l1lD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1620 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2

结构域编号 domain_id	1l1lD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1390 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3

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7. 引用文献 (1)

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晶胞边长 a length_a	120.500 Å
晶胞边长 b length_b	114.700 Å
晶胞边长 c length_c	121.300 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.20 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.750 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2230
R_free r_free	0.2660

fit	/app/data/saxs_computation/l1/1l1l/1l1l.fit
pddf	/app/data/pr_computation/l1/1l1l/1l1l.pr.out
profile	/app/data/saxs_computation/l1/1l1l/1l1l.dat

CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE

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