1qh1

NITROGENASE MOFE PROTEIN FROM KLEBSIELLA PNEUMONIAE, PHENOSAFRANIN OXIDIZED STATE

Method: X-RAY DIFFRACTION D_max: 120.3 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	1qh1
沉积日期 deposition_date	1999-05-10
结构标题 title	NITROGENASE MOFE PROTEIN FROM KLEBSIELLA PNEUMONIAE, PHENOSAFRANIN OXIDIZED STATE
关键词 keywords	BIOLOGICAL NITROGEN FIXATION, NITROGEN METABOLISM, MOLYBDOENZYMES, ELECTRON TRANSFER, 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	38.21 Å
回转半径 Rg (电子) rg_electron	37.55 Å
零角强度 I(0) i0	767459000.00
分子量 molecular_weight	224210.0 kDa
排除体积 excluded_volume	278470 Å³
包络体积 envelope_volume	324630 Å³
水化壳体积 shell_volume	68769 Å³
包络直径 envelope_diameter	121.9 Å
壳层 Rg shell_rg	45.90 Å
包络 Rg envelope_rg	37.53 Å
形状 Rg shape_rg	37.57 Å
总 Rg total_rg	37.90 Å
总原子数 total_atoms	15628
残基数 n_residues	1994
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	120.3 Å
Rg (实空间) rg_real	38.10 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	7.6750e+08
I(0) 误差 (实空间) i0_real_error	1.4450e+07
Rg (倒空间) rg_reciprocal	38.17 Å
I(0) (倒空间) i0_reciprocal	767500000.0000
解质量估计 total_estimate	0.8922
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	44.0 Å
偏度 Skewness skewness	0.256
峰度 Kurtosis kurtosis	-0.533
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	253700000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.806

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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 (9)

Entity 1 polymer

描述 description	PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN)
分子量 formula_weight	53632.1 kDa
EC 编号 ec_number	1.18.6.1
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	18303

TNATGERNLALIQEVLEVFPETARKERRKHMMVSDPKMKSVGKCIISNRKSQPGVMTVRGCAYAGSKGVVFGPIKDMAHISHGPVGCGQYSRAGRRNYYTGVSGVDSFGTLNFTSDFQERDIVFGGDKKLSKLIEEMELLFPLTKGITIQSECPVGLIGDDISAVANASSKALDKPVIPVRCEGFRGVSQSLGHHIANDVVRDWILNNREGQPFETTPYDVAIIGDYNIGGDAWASRILLEEMGLRVVAQWSGDGTLVEMENTPFVKLNLVHCYRSMNYIARHMEEKHQIPWMEYNFFGPTKIAESLRKIADQFDDTIRANAEAVIARYEGQMAAIIAKYRPRLEGRKVLLYMGGLRPRHVIGAYEDLGMEIIAAGYEFAHNDDYDRTLPDLKEGTLLFDDASSYELEAFVKALKPDLIGSGIKEKYIFQKMGVPFRQMHSWDYSGPYHGYDGFAIFARDMDMTLNNPAWNELTAPWL

Entity 2 polymer

描述 description	PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN)
分子量 formula_weight	58338.2 kDa
EC 编号 ec_number	1.18.6.1
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

SQTIDKINSCYPLFEQDEYQELFRNKRQLEEAHDAQRVQEVFAWTTTAEYEALNFRREALTVDPAKACQPLGAVLCSLGFANTLPYVHGSQGCVAYFRTYFNRHFKEPIACVSDSMTEDAAVFGGNNNMNLGLQNASALYKPEIIAVSTTCMAEVIGDDLQAFIANAKKDGFVDSSIAVPHAHTPSFIGSHVTGWDNMFEGFAKTFTADYQGQPGKLPKLNLVTGFETYLGNFRVLKRMMEQMAVPCSLLSDPSEVLDTPADGHYRMYSGGTTQQEMKEAPDAIDTLLLQPWQLLKSKKVVQEMWNQPATEVAIPLGLAATDELLMTVSQLSGKPIADALTLERGRLVDMMLDSHTWLHGKKFGLYGDPDFVMGLTRFLLELGCEPTVILSHNANKRWQKAMNKMLDASPYGRDSEVFINCDLWHFRSLMFTRQPDFMIGNSYGKFIQRDTLAKGKAFEVPLIRLGFPLFDRHHLHRQTTWGYEGAMNIVTTLVNAVLEKLDSDTSQLGKTDYSFDLVR

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 non-polymer

描述 description	3-HYDROXY-3-CARBOXY-ADIPIC ACID
分子量 formula_weight	206.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	FE-MO-S CLUSTER
分子量 formula_weight	775.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	FE(8)-S(7) CLUSTER
分子量 formula_weight	671.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	13

Entity 8 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	2

Entity 9 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	2622

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1qh1a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.92 — Chelatase-like
超家族 Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
家族 Family family	c.92.2.3 — Nitrogenase iron-molybdenum protein

结构域编号 domain_id	d1qh1b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.92 — Chelatase-like
超家族 Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
家族 Family family	c.92.2.3 — Nitrogenase iron-molybdenum protein

结构域编号 domain_id	d1qh1c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.92 — Chelatase-like
超家族 Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
家族 Family family	c.92.2.3 — Nitrogenase iron-molybdenum protein

结构域编号 domain_id	d1qh1d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.92 — Chelatase-like
超家族 Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
家族 Family family	c.92.2.3 — Nitrogenase iron-molybdenum protein

CATH v4.4 (14 domains)

结构域编号 domain_id	1qh1A01
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1A02
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1A03
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1B01
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1B02
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1B03
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1B04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	89 — Nitrogenase Molybdenum-iron Protein, subunit B; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Nitrogenase Molybdenum-iron Protein, subunit B, domain 4

结构域编号 domain_id	1qh1C01
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1C02
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1C03
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1D01
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1D02
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1D03
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	1980 — Nitrogenase molybdenum iron protein domain

结构域编号 domain_id	1qh1D04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	89 — Nitrogenase Molybdenum-iron Protein, subunit B; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Nitrogenase Molybdenum-iron Protein, subunit B, domain 4

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7. 引用文献 (1)

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晶胞边长 a length_a	204.180 Å
晶胞边长 b length_b	75.220 Å
晶胞边长 c length_c	162.840 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	122.88 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.1580
R_free r_free	0.1990

fit	/app/data/saxs_computation/qh/1qh1/1qh1.fit
pddf	/app/data/pr_computation/qh/1qh1/1qh1.pr.out
profile	/app/data/saxs_computation/qh/1qh1/1qh1.dat

NITROGENASE MOFE PROTEIN FROM KLEBSIELLA PNEUMONIAE, PHENOSAFRANIN OXIDIZED STATE

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

衍射实验 Diffraction

5. 实体与聚合体信息 (9)

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 non-polymer

Entity 8 non-polymer

Entity 9 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

CATH v4.4 (14 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)