1tzl

Crystal Structure of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp.

Method: X-RAY DIFFRACTION D_max: 217.3 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	1tzl
沉积日期 deposition_date	2004-07-10
结构标题 title	Crystal Structure of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp.
关键词 keywords	GMC oxidoreductase, glucose-methanol-choline family, large inner cavity, 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	63.88 Å
回转半径 Rg (电子) rg_electron	63.97 Å
零角强度 I(0) i0	4225580000.00
分子量 molecular_weight	529290.0 kDa
排除体积 excluded_volume	650700 Å³
包络体积 envelope_volume	912840 Å³
水化壳体积 shell_volume	115570 Å³
包络直径 envelope_diameter	207.0 Å
壳层 Rg shell_rg	68.31 Å
包络 Rg envelope_rg	62.12 Å
形状 Rg shape_rg	63.99 Å
总 Rg total_rg	63.94 Å
总原子数 total_atoms	36816
残基数 n_residues	4488
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	217.3 Å
Rg (实空间) rg_real	64.02 Å
Rg 误差 (实空间) rg_real_error	3.11 Å
I(0) (实空间) i0_real	4.2260e+09
I(0) 误差 (实空间) i0_real_error	1.0080e+08
Rg (倒空间) rg_reciprocal	63.68 Å
I(0) (倒空间) i0_reciprocal	4223000000.0000
解质量估计 total_estimate	0.8521
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	60.9 Å
偏度 Skewness skewness	0.256
峰度 Kurtosis kurtosis	-0.814
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	396800000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.807

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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 (3)

Entity 1 polymer

描述 description	pyranose oxidase
分子量 formula_weight	70032.9 kDa
EC 编号 ec_number	1.1.3.10
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	38970

STSSSDPFFNFAKSSFRSAAAQKASASSLPPLPGPDKKVPGMDIKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTHWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLAEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPTNPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMEPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPFTSEAQ

来源 Source

来源生物 organism	Peniophora sp. SG
NCBI 分类编号 ncbi_taxonomy_id	204723
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	8

Entity 3 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	2154

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1tzla1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1tzla2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1tzlb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1tzlb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1tzlc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1tzlc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1tzld1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1tzld2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1tzle1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1tzle2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1tzlf1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1tzlf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1tzlg1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1tzlg2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1tzlh1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1tzlh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

CATH v4.4 (8 domains)

结构域编号 domain_id	1tzlA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1tzlB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1tzlC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1tzlD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1tzlE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1tzlF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1tzlG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1tzlH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
同源超家族 H-superfamily homologous superfamily	50 —

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7. 引用文献 (1)

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晶胞边长 a length_a	164.879 Å
晶胞边长 b length_b	103.596 Å
晶胞边长 c length_c	169.169 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.25 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.350 Å
最低分辨率 resolution_low	19.700 Å
R 因子 r_factor	0.1760
R_work r_work	0.1740
R_free r_free	0.2258

fit	/app/data/saxs_computation/tz/1tzl/1tzl.fit
pddf	/app/data/pr_computation/tz/1tzl/1tzl.pr.out
profile	/app/data/saxs_computation/tz/1tzl/1tzl.dat