1kif

D-AMINO ACID OXIDASE FROM PIG KIDNEY

Method: X-RAY DIFFRACTION D_max: 174.6 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	1kif
沉积日期 deposition_date	1996-01-19
结构标题 title	D-AMINO ACID OXIDASE FROM PIG KIDNEY
关键词 keywords	FAD COFACTOR, OXIDASE, FLAVOENZYME, FLAVOPROTEIN; FLAVOPROTEIN
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	50.73 Å
回转半径 Rg (电子) rg_electron	50.50 Å
零角强度 I(0) i0	1392220000.00
分子量 molecular_weight	314780.0 kDa
排除体积 excluded_volume	394720 Å³
包络体积 envelope_volume	516090 Å³
水化壳体积 shell_volume	84975 Å³
包络直径 envelope_diameter	186.3 Å
壳层 Rg shell_rg	54.34 Å
包络 Rg envelope_rg	49.74 Å
形状 Rg shape_rg	50.49 Å
总 Rg total_rg	50.66 Å
总原子数 total_atoms	22256
残基数 n_residues	2712
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	174.6 Å
Rg (实空间) rg_real	50.83 Å
Rg 误差 (实空间) rg_real_error	2.05 Å
I(0) (实空间) i0_real	1.3920e+09
I(0) 误差 (实空间) i0_real_error	2.9430e+07
Rg (倒空间) rg_reciprocal	50.64 Å
I(0) (倒空间) i0_reciprocal	1392000000.0000
解质量估计 total_estimate	0.8600
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	56.3 Å
偏度 Skewness skewness	0.422
峰度 Kurtosis kurtosis	-0.297
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	69320000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.753

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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	D-AMINO ACID OXIDASE
分子量 formula_weight	39377.8 kDa
EC 编号 ec_number	1.4.3.3
来源方法 src_method	nat
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	22550

MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPYIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFRPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLLTMPPSHL

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 non-polymer

描述 description	BENZOIC ACID
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	294

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1kifa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

结构域编号 domain_id	d1kifa2
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.16.1.3 — D-aminoacid oxidase-like

结构域编号 domain_id	d1kifb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

结构域编号 domain_id	d1kifb2
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.16.1.3 — D-aminoacid oxidase-like

结构域编号 domain_id	d1kifc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

结构域编号 domain_id	d1kifc2
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.16.1.3 — D-aminoacid oxidase-like

结构域编号 domain_id	d1kifd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

结构域编号 domain_id	d1kifd2
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.16.1.3 — D-aminoacid oxidase-like

结构域编号 domain_id	d1kife1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

结构域编号 domain_id	d1kife2
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.16.1.3 — D-aminoacid oxidase-like

结构域编号 domain_id	d1kiff1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

结构域编号 domain_id	d1kiff2
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.16.1.3 — D-aminoacid oxidase-like

结构域编号 domain_id	d1kifg1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

结构域编号 domain_id	d1kifg2
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.16.1.3 — D-aminoacid oxidase-like

结构域编号 domain_id	d1kifh1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

结构域编号 domain_id	d1kifh2
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.16.1.3 — D-aminoacid oxidase-like

CATH v4.4 (16 domains)

结构域编号 domain_id	1kifA01
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	1kifA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1kifB01
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	1kifB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1kifC01
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	1kifC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1kifD01
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	1kifD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1kifE01
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	1kifE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1kifF01
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	1kifF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1kifG01
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	1kifG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	1kifH01
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	1kifH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	326.480 Å
晶胞边长 b length_b	138.100 Å
晶胞边长 c length_c	200.850 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	64

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ki/1kif/1kif.fit
pddf	/app/data/pr_computation/ki/1kif/1kif.pr.out
profile	/app/data/saxs_computation/ki/1kif/1kif.dat