SAXSdb — 2ipi

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ipi
沉积日期 deposition_date	2006-10-12
结构标题 title	Crystal Structure of Aclacinomycin Oxidoreductase
关键词 keywords	anthracycline, aclacinomycin, oxidoreductase, flavoenzyme, twinning, MAD; 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	49.89 Å
回转半径 Rg (电子) rg_electron	49.91 Å
零角强度 I(0) i0	727263000.00
分子量 molecular_weight	219960.0 kDa
排除体积 excluded_volume	272720 Å³
包络体积 envelope_volume	367840 Å³
水化壳体积 shell_volume	60408 Å³
包络直径 envelope_diameter	155.0 Å
壳层 Rg shell_rg	55.65 Å
包络 Rg envelope_rg	48.11 Å
形状 Rg shape_rg	49.89 Å
总 Rg total_rg	50.17 Å
总原子数 total_atoms	15562
残基数 n_residues	1968
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	143.0 Å
Rg (实空间) rg_real	50.10 Å
Rg 误差 (实空间) rg_real_error	1.07 Å
I(0) (实空间) i0_real	7.2730e+08
I(0) 误差 (实空间) i0_real_error	1.2010e+07
Rg (倒空间) rg_reciprocal	49.90 Å
I(0) (倒空间) i0_reciprocal	727100000.0000
解质量估计 total_estimate	0.8118
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	40.2 Å
偏度 Skewness skewness	0.216
峰度 Kurtosis kurtosis	-0.995
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	69600000.0000
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: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.000

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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	Aclacinomycin oxidoreductase (AknOx)
分子量 formula_weight	57221.8 kDa
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	16589

MAHHHHHHHRSAAGTIWEFDGGACGARTALVKVDRVDRRYQDLVTRGFNGRFRGRPDVVYVVHTADQVVDAVNQAMAAGQRIAVRSGGHCFEGFVDDPAVRAVIDMSQMRQVFYDSGKRAFAVEPGATLGETYRALYLDWGVTIPAGVCPQVGVGGHVLGGGYGPLSRRDGVVADHLYAVEVVVVDASGRARKVVATSAADDPNRELWWAHTGGGGGNFGIVTRYWFRTPGATGTDPSQLLPKAPTSTLRHIVTWDWSALTEEAFTRIIDNHGAWHQSNSAAGTPYASMHSVFYLNSRAAGQILLDIQIDGGLDGAEALLNDFVAAVNEGTGVEPAVQRSTEPWLRATLANKFDTGGFDRTKSKGAYLRKPWTAAQAATLYRHLSADSQVWGEVSLYSYGGKVNSVPETATATAQRDSIIKVWMSATWMDPAHDDANLAWIREIYREIFATTGGVPVPDDRTEGTFINYPDVDLVDERWNTSGVPWYTLYYKGNYPRLQKVKARWDPRDVFRHALSVRPPG

来源 Source

来源生物 organism	Streptomyces galilaeus
NCBI 分类编号 ncbi_taxonomy_id	33899
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;METHYL (2S,4R)-2-ETHYL-2,5,7-TRIHYDROXY-6,11-DIOXO-4-{[2,3,6-TRIDEOXY-4-O-{2,6-DIDEOXY-4-O-[(2S,6S)-6-METHYL-5-OXOTETRAHYDRO-2H -PYRAN-2-YL]-ALPHA-D-LYXO-HEXOPYRANOSYL}-3-(DIMETHYLAMINO)-D-RIBO-HEXOPYRANOSYL]OXY}-1,2,3,4,6,11-HEXAHYDROTETRACENE-1-C ARBOXYLATE ;
分子量 formula_weight	811.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	1009

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2ipiA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2ipiA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2ipiB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2ipiB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2ipiC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2ipiC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2ipiD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2ipiD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (1)

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晶胞边长 a length_a	68.500 Å
晶胞边长 b length_b	266.200 Å
晶胞边长 c length_c	68.700 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	119.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.650 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1850
R_work r_work	—
R_free r_free	0.2420

fit	/app/data/saxs_computation/ip/2ipi/2ipi.fit
pddf	/app/data/pr_computation/ip/2ipi/2ipi.pr.out
profile	/app/data/saxs_computation/ip/2ipi/2ipi.dat

Crystal Structure of Aclacinomycin Oxidoreductase

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