SAXSdb — 2iwk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2iwk
沉积日期 deposition_date	2006-06-30
结构标题 title	Inhibitor-bound form of nitrous oxide reductase from Achromobacter Cycloclastes at 1.7 Angstrom resolution
关键词 keywords	;METAL-BINDING, OXIDOREDUCTASE, DENITRIFICATION, NITROUS OXIDE BINDING, CATALYSIS, PERIPLASMIC ELECTRON GATING, COPPER CHEMISTRY, CALCIUM, COPPER ;; 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	30.92 Å
回转半径 Rg (电子) rg_electron	30.46 Å
零角强度 I(0) i0	311083000.00
分子量 molecular_weight	136610.0 kDa
排除体积 excluded_volume	167440 Å³
包络体积 envelope_volume	188720 Å³
水化壳体积 shell_volume	49407 Å³
包络直径 envelope_diameter	112.1 Å
壳层 Rg shell_rg	39.36 Å
包络 Rg envelope_rg	30.93 Å
形状 Rg shape_rg	30.49 Å
总 Rg total_rg	31.01 Å
总原子数 total_atoms	9355
残基数 n_residues	1180
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	104.8 Å
Rg (实空间) rg_real	30.86 Å
Rg 误差 (实空间) rg_real_error	0.66 Å
I(0) (实空间) i0_real	3.1110e+08
I(0) 误差 (实空间) i0_real_error	4.6500e+06
Rg (倒空间) rg_reciprocal	30.89 Å
I(0) (倒空间) i0_reciprocal	311100000.0000
解质量估计 total_estimate	0.6678
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	34.9 Å
偏度 Skewness skewness	0.351
峰度 Kurtosis kurtosis	-0.230
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	222800000.0000
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: 0.789; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.991; Smooth: 0.973

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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 (8)

Entity 1 polymer

描述 description	NITROUS OXIDE REDUCTASE
分子量 formula_weight	70993.1 kDa
EC 编号 ec_number	1.7.99.6
来源方法 src_method	nat
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	10214

MESKEHKGLSRRALFSATAGSAILAGTVGPAALSLGAAGLATPARAATGADGSVAPGKLDDYYGFWSSGQTGEMRILGIPSMRELMRVPVFNRCSATGWGQTNESIRIHQRTMTEKTKKQLAANGKKIHDNGDLHHVHMSFTDGKYDGRYLFMNDKANTRVARVRCDVMKTDAILEIPNAKGIHGMRPQKWPRSNYVFCNGEDEAPLVNDGSTMTDVATYVNIFTAVDADKWEVAWQVKVSGNLDNCDADYEGKWAFSTSYNSEMGMTLEEMTKSEMDHVVVFNIAEIEKAIKAGQYEEINGVKVVDGRKEAKSLFTRYIPIANNPHGCNMAPDRKHLCVAGKLSPTVTVLDVTKFDALFYDNAEPRSAVVAEPELGLGPLHTAFDGRGNAYTSLFLDSQVVKWNIDEAIRAYAGEKINPIKDKLDVQYQPGHLKTVMGETLDAANDWLVCLCKFSKDRFLNVGPLKPENDQLIDISGDKMVLVHDGPTFAEPHDAIAVSPSILPNIRSVWDRNDPLWAETRKQAEADEVDIDEWTEAVIRDGNKVRVYMTSVAPSFSQPSFTVKEGDEVTVIVTNLDEIDDLTHGFTMGNHGVAMEVGPQQTSSVTFVAANPGVYWYYCQWFCHALHMEMRGRMFVEPKGA

Entity 2 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
分子量 formula_weight	286.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	IODIDE ION
分子量 formula_weight	126.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

Entity 5 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	28

Entity 6 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 7 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	30

Entity 8 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	853

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2iwka1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.3 — Nitrous oxide reductase, N-terminal domain
家族 Family family	b.69.3.1 — Nitrous oxide reductase, N-terminal domain

结构域编号 domain_id	d2iwka2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.0 — automated matches

结构域编号 domain_id	d2iwkb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.3 — Nitrous oxide reductase, N-terminal domain
家族 Family family	b.69.3.1 — Nitrous oxide reductase, N-terminal domain

结构域编号 domain_id	d2iwkb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2iwkA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2iwkA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	2iwkB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2iwkB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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7. 引用文献 (1)

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晶胞边长 a length_a	71.114 Å
晶胞边长 b length_b	120.913 Å
晶胞边长 c length_c	137.343 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1700
R_work r_work	0.1680
R_free r_free	0.2070

fit	/app/data/saxs_computation/iw/2iwk/2iwk.fit
pddf	/app/data/pr_computation/iw/2iwk/2iwk.pr.out
profile	/app/data/saxs_computation/iw/2iwk/2iwk.dat

Inhibitor-bound form of nitrous oxide reductase from Achromobacter Cycloclastes at 1.7 Angstrom resolution

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution