1mio

X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION D_max: 128.8 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	1mio
沉积日期 deposition_date	1993-03-24
结构标题 title	X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION
关键词 keywords	MOLYBDENUM-IRON PROTEIN; MOLYBDENUM-IRON PROTEIN
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	39.63 Å
回转半径 Rg (电子) rg_electron	39.12 Å
零角强度 I(0) i0	724815000.00
分子量 molecular_weight	219400.0 kDa
排除体积 excluded_volume	273230 Å³
包络体积 envelope_volume	328100 Å³
水化壳体积 shell_volume	67688 Å³
包络直径 envelope_diameter	130.1 Å
壳层 Rg shell_rg	46.55 Å
包络 Rg envelope_rg	39.14 Å
形状 Rg shape_rg	39.12 Å
总 Rg total_rg	39.45 Å
总原子数 total_atoms	15269
残基数 n_residues	1964
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	128.8 Å
Rg (实空间) rg_real	39.59 Å
Rg 误差 (实空间) rg_real_error	0.87 Å
I(0) (实空间) i0_real	7.2480e+08
I(0) 误差 (实空间) i0_real_error	1.1940e+07
Rg (倒空间) rg_reciprocal	39.62 Å
I(0) (倒空间) i0_reciprocal	724800000.0000
解质量估计 total_estimate	0.8926
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	41.9 Å
偏度 Skewness skewness	0.283
峰度 Kurtosis kurtosis	-0.587
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	265800000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.907

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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	NITROGENASE MOLYBDENUM IRON PROTEIN (ALPHA CHAIN)
分子量 formula_weight	59071.2 kDa
来源方法 src_method	man
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	15269

SENLKDEILEKYIPKTKKTRSGHIVIKTEETPNPEIVANTRTVPGIITARGCAYAGCKGVVMGPIKDMVHITHGPIGCSFYTWGGRRFKSKPENGTGLNFNEYVFSTDMQESDIVFGGVNKLKDAIHEAYEMFHPAAIGVYATCPVGLIGDDILAVAATASKEIGIPVHAFSCEGYKGVSQSAGHHIANNTVMTDIIGKGNKEQKKYSINVLGEYNIGGDAWEMDRVLEKIGYHVNATLTGDATYEKVQNADKADLNLVQCHRSINYIAEMMETKYGIPWIKCNFIGVDGIVETLRDMAKCFDDPELTKRTEEVIAEEIAAIQDDLDYFKEKLQGKTACLYVGGSRSHTYMNMLKSFGVDSLVAGFEFAHRDDYEGREVIPTIKIDADSKNIPEITVTPDEQKYRVVIPEDKVEELKKAGVPLSSYGGMMKEMHDGTILIDDMNHHDMEVVLEKLKPDMFFAGIKEKFVIQKGGVLSKQLHSYDYNGPYAGFRGVVNFGHELVNGIYTPAWKMITPPWKKASSESKVVVGGEA

来源 Source

来源生物 organism	Clostridium pasteurianum
NCBI 分类编号 ncbi_taxonomy_id	1501

Entity 2 polymer

描述 description	NITROGENASE MOLYBDENUM IRON PROTEIN (BETA CHAIN)
分子量 formula_weight	50175.1 kDa
来源方法 src_method	man
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

MLDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHSHGSQGCCSYHRTVLSRHFKEPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDIIAVHTTCLSETLGDDLPTYISQMEDAGSIPEGKLVIHTNTPSYVGSHVTGFANMVQGIVNYLSENTGAKNGKINVIPGFVGPADMREIKRLFEAMDIPYIMFPDTSGVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSLGSYASDLGAKTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASIEEERGQLIDLMIDAQQYLQGKKVALLGDPDEIIALSKFIIELGAIPKYVVTGTPGMKFQKEIDAMLAEAGIEGSKVKVEGDFFDVHQWIKNEGVDLLISNTYGKFIAREENIPFVRFGFPIMDRYGHYYNPKVGYKGAIRLVEEITNVILDKIERECTEEDFEVVR

来源 Source

来源生物 organism	Clostridium pasteurianum
NCBI 分类编号 ncbi_taxonomy_id	1501

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	2

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-S CLUSTER
分子量 formula_weight	703.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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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	d1mioa_
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	d1miob_
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	d1mioc_
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	d1miod_
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	1mioA01
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	1mioA02
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	1mioA03
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	1mioB01
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	1mioB02
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	1mioB03
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	1mioB04
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	1mioC01
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	1mioC02
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	1mioC03
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	1mioD01
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	1mioD02
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	1mioD03
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	1mioD04
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

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7. 引用文献 (3)

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晶胞边长 a length_a	69.960 Å
晶胞边长 b length_b	151.300 Å
晶胞边长 c length_c	121.900 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.40 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	3.000 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.1800
R_work r_work	0.1800
R_free r_free	—

fit	/app/data/saxs_computation/mi/1mio/1mio.fit
pddf	/app/data/pr_computation/mi/1mio/1mio.pr.out
profile	/app/data/saxs_computation/mi/1mio/1mio.dat

X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

CATH v4.4 (14 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)