1r27

Crystal Structure of NarGH complex

Method: X-RAY DIFFRACTION D_max: 188.8 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	1r27
沉积日期 deposition_date	2003-09-26
结构标题 title	Crystal Structure of NarGH complex
关键词 keywords	beta barrel; x-ray crystallography, 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	53.57 Å
回转半径 Rg (电子) rg_electron	53.71 Å
零角强度 I(0) i0	2255940000.00
分子量 molecular_weight	386420.0 kDa
排除体积 excluded_volume	477640 Å³
包络体积 envelope_volume	582600 Å³
水化壳体积 shell_volume	90090 Å³
包络直径 envelope_diameter	189.0 Å
壳层 Rg shell_rg	56.38 Å
包络 Rg envelope_rg	53.27 Å
形状 Rg shape_rg	53.62 Å
总 Rg total_rg	54.04 Å
总原子数 total_atoms	27010
残基数 n_residues	3366
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	188.8 Å
Rg (实空间) rg_real	53.84 Å
Rg 误差 (实空间) rg_real_error	2.27 Å
I(0) (实空间) i0_real	2.2560e+09
I(0) 误差 (实空间) i0_real_error	4.3440e+07
Rg (倒空间) rg_reciprocal	53.33 Å
I(0) (倒空间) i0_reciprocal	2254000000.0000
解质量估计 total_estimate	0.8238
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	45.6 Å
偏度 Skewness skewness	0.440
峰度 Kurtosis kurtosis	-0.538
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	502100000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.682; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.737

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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 (7)

Entity 1 polymer

描述 description	Respiratory nitrate reductase 1 alpha chain
分子量 formula_weight	140526.8 kDa
EC 编号 ec_number	1.7.99.4
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,C
原子数 atom_count	29331

SKFLDRFRYFKQKGETFADGHGQLLNTNRDWEDGYRQRWQHDKIVRSTHGVNCTGSCSWKIYVKNGLVTWETQQTDYPRTRPDLPNHEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWASIIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDRVAGFSPIPAMSMVSYASGARYLSLIGGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGSNVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYTDMPMLVMLEERDGYYAAGRMLRAADLVDALGQENNPEWKTVAFNTNGEMVAPNGSIGFRWGEKGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDLTLANYGLERGLNDVNCATSYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMADKSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEKDDMNTSDMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKDWKKGECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDAAEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHELIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSVKEVIGQKSNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLGRGGPVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGMTMMYHAQERIVNLPGSEITQQRGGIHNSVTRITPKPTHMIGGYAHLAYGFNYYGTVGSNRDEFVVVRKMKNIDWLDGEGNDQVQESVK

Entity 2 polymer

描述 description	Respiratory nitrate reductase 1 beta chain
分子量 formula_weight	58140.3 kDa
EC 编号 ec_number	1.7.99.4
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	B,D

MKIRSQVGMVLNLDKCIGCHTCSVTCKNVWTSREGVEYAWFNNVETKPGQGFPTDWENQEKYKGGWIRKINGKLQPRMGNRAMLLGKIFANPHLPGIDDYYEPFDFDYQNLHTAPEGSKSQPIARPRSLITGERMAKIEKGPNWEDDLGGEFDKLAKDKNFDNIQKAMYSQFENTFMMYLPRLCEHCLNPACVATCPSGAIYKREEDGIVLIDQDKCRGWRMCITGCPYKKIYFNWKSGKSEKCIFCYPRIEAGQPTVCSETCVGRIRYLGVLLYDADAIERAASTENEKDLYQRQLDVFLDPNDPKVIEQAIKDGIPLSVIEAAQQSPVYKMAMEWKLALPLHPEYRTLPMVWYVPPLSPIQSAADAGELGSNGILPDVESLRIPVQYLANLLTAGDTKPVLRALKRMLAMRHYKRAETVDGKVDTRALEEVGLTEAQAQEMYRYLAIANYEDRFVVPSSHRELAREAFPEKNGCGFTFGDGCHGSDTKFNLFNSRRIDAIDVTSKTEPHP

Entity 3 non-polymer

描述 description	MOLYBDENUM ATOM
分子量 formula_weight	95.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 5 non-polymer

描述 description	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
分子量 formula_weight	740.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	FE3-S4 CLUSTER
分子量 formula_weight	295.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	2321

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1r27a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

结构域编号 domain_id	d1r27a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
超家族 Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
家族 Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

结构域编号 domain_id	d1r27b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
家族 Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

结构域编号 domain_id	d1r27c1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

结构域编号 domain_id	d1r27c2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
超家族 Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
家族 Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

结构域编号 domain_id	d1r27d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
家族 Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

CATH v4.4 (8 domains)

结构域编号 domain_id	1r27A02
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	12770 — Nitrate reductase alpha subunit

结构域编号 domain_id	1r27A04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1r27B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1r27B03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3650 — nitrate reductase domain fold
同源超家族 H-superfamily homologous superfamily	10 — nitrate reductase domain like

结构域编号 domain_id	1r27C02
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	12770 — Nitrate reductase alpha subunit

结构域编号 domain_id	1r27C04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1r27D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1r27D03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3650 — nitrate reductase domain fold
同源超家族 H-superfamily homologous superfamily	10 — nitrate reductase domain like

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7. 引用文献 (1)

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晶胞边长 a length_a	127.401 Å
晶胞边长 b length_b	298.300 Å
晶胞边长 c length_c	296.853 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	16

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	39.860 Å
R 因子 r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2300

fit	/app/data/saxs_computation/r2/1r27/1r27.fit
pddf	/app/data/pr_computation/r2/1r27/1r27.pr.out
profile	/app/data/saxs_computation/r2/1r27/1r27.dat

Crystal Structure of NarGH complex

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

5. 实体与聚合体信息 (7)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)