1fwx

CRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS

Method: X-RAY DIFFRACTION D_max: 173.1 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	1fwx
沉积日期 deposition_date	2000-09-25
结构标题 title	CRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS
关键词 keywords	Beta-propeller domain, cupredoxin domain, CuZ site, CuA site, 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	49.12 Å
回转半径 Rg (电子) rg_electron	49.86 Å
零角强度 I(0) i0	1089890000.00
分子量 molecular_weight	265320.0 kDa
排除体积 excluded_volume	327260 Å³
包络体积 envelope_volume	401180 Å³
水化壳体积 shell_volume	69006 Å³
包络直径 envelope_diameter	180.8 Å
壳层 Rg shell_rg	50.44 Å
包络 Rg envelope_rg	49.54 Å
形状 Rg shape_rg	49.89 Å
总 Rg total_rg	49.79 Å
总原子数 total_atoms	18534
残基数 n_residues	2358
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	173.1 Å
Rg (实空间) rg_real	49.74 Å
Rg 误差 (实空间) rg_real_error	2.24 Å
I(0) (实空间) i0_real	1.0900e+09
I(0) 误差 (实空间) i0_real_error	2.3700e+07
Rg (倒空间) rg_reciprocal	49.13 Å
I(0) (倒空间) i0_reciprocal	1089000000.0000
解质量估计 total_estimate	0.7866
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	43.3 Å
偏度 Skewness skewness	0.516
峰度 Kurtosis kurtosis	-0.484
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	164600000.0000
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: 0.627; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.698; Smooth: 0.642

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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 (6)

Entity 1 polymer

描述 description	NITROUS OXIDE REDUCTASE
分子量 formula_weight	66397.5 kDa
EC 编号 ec_number	1.7.99.6
来源方法 src_method	nat
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	21176

ASADGSVAPGQLDDYYGFWSSGQSGEMRILGIPSMRELMRVPVFNRCSATGWGQTNESVRIHERTMSERTKKFLAANGKRIHDNGDLHHVHMSFTEGKYDGRFLFMNDKANTRVARVRCDVMKCDAILEIPNAKGIHGLRPQKWPRSNYVFCNGEDETPLVNDGTNMEDVANYVNVFTAVDADKWEVAWQVLVSGNLDNCDADYEGKWAFSTSYNSEKGMTLPEMTAAEMDHIVVFNIAEIEKAIAAGDYQELNGVKVVDGRKEASSLFTRYIPIANNPHGCNMAPDKKHLCVAGKLSPTVTVLDVTRFDAVFYENADPRSAVVAEPELGLGPLHTAFDGRGNAYTSLFLDSQVVKWNIEDAIRAYAGEKVDPIKDKLDVHYQPGHLKTVMGETLDATNDWLVCLSKFSKDRFLNVGPLKPENDQLIDISGDKMVLVHDGPTFAEPHDAIAVHPSILSDIKSVWDRNDPMWAETRAQAEADGVDIDNWTEEVIRDGNKVRVYMSSVAPSFSIESFTVKEGDEVTVIVTNLDEIDDLTHGFTMGNYGVAMEIGPQMTSSVTFVAANPGVYWYYCQWFCHALHMEMRGRMLVEPKEA

Entity 2 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	4

Entity 3 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	11

Entity 4 non-polymer

描述 description	DINUCLEAR COPPER ION
分子量 formula_weight	127.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	4

Entity 6 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	2642

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1fwxa1
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.6.1.4 — Nitrosocyanin

结构域编号 domain_id	d1fwxa2
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	d1fwxb1
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.6.1.4 — Nitrosocyanin

结构域编号 domain_id	d1fwxb2
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	d1fwxc1
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.6.1.4 — Nitrosocyanin

结构域编号 domain_id	d1fwxc2
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	d1fwxd1
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.6.1.4 — Nitrosocyanin

结构域编号 domain_id	d1fwxd2
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

CATH v4.4 (8 domains)

结构域编号 domain_id	1fwxA01
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	1fwxA02
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	1fwxB01
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	1fwxB02
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	1fwxC01
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	1fwxC02
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	1fwxD01
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	1fwxD02
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 (2)

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晶胞边长 a length_a	102.595 Å
晶胞边长 b length_b	105.090 Å
晶胞边长 c length_c	116.696 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.69 °
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	1.600 Å
最低分辨率 resolution_low	29.830 Å
R 因子 r_factor	0.2630
R_work r_work	0.2410
R_free r_free	0.2640

fit	/app/data/saxs_computation/fw/1fwx/1fwx.fit
pddf	/app/data/pr_computation/fw/1fwx/1fwx.pr.out
profile	/app/data/saxs_computation/fw/1fwx/1fwx.dat