SAXSdb — 1mhz

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mhz
沉积日期 deposition_date	1996-10-21
结构标题 title	METHANE MONOOXYGENASE HYDROXYLASE
关键词 keywords	OXIDOREDUCTASE, MONOOXYGENASE, NADP, ONE-CARBON METABOLISM; 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	30.21 Å
回转半径 Rg (电子) rg_electron	29.60 Å
零角强度 I(0) i0	226895000.00
分子量 molecular_weight	121360.0 kDa
排除体积 excluded_volume	151860 Å³
包络体积 envelope_volume	170870 Å³
水化壳体积 shell_volume	46384 Å³
包络直径 envelope_diameter	103.6 Å
壳层 Rg shell_rg	38.21 Å
包络 Rg envelope_rg	29.82 Å
形状 Rg shape_rg	29.59 Å
总 Rg total_rg	30.31 Å
总原子数 total_atoms	10530
残基数 n_residues	1060
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	97.1 Å
Rg (实空间) rg_real	30.13 Å
Rg 误差 (实空间) rg_real_error	0.52 Å
I(0) (实空间) i0_real	2.2690e+08
I(0) 误差 (实空间) i0_real_error	3.3100e+06
Rg (倒空间) rg_reciprocal	30.17 Å
I(0) (倒空间) i0_reciprocal	226900000.0000
解质量估计 total_estimate	0.8838
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.3 Å
偏度 Skewness skewness	0.323
峰度 Kurtosis kurtosis	-0.270
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	77220000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.891

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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 (5)

Entity 1 polymer

描述 description	METHANE MONOOXYGENASE HYDROXYLASE
分子量 formula_weight	45165.1 kDa
EC 编号 ec_number	1.14.13.25
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B
原子数 atom_count	10542

MSQPQSSQVTKRGLTDPERAAIIAAAVPDHALDTQRKYHYFIQPRWKPLSEYEQLSCYAQPNPDWIAGGLDWGDWTQKFHGGRPSWGNESTELRTTDWYRHRDPARRWHHPYVKDKSEEARYTQRFLAAYSSEGSIRTIDPYWRDEILNKYFGALLYSEYGLFNAHSSVGRDCLSDTIRQTAVFAALDKVDNAQMIQMERLFIAKLVPGFDASTDVPKKIWTTDPIYSGARATVQEIWQGVQDWNEILWAGHAVYDATFGQFARREFFQRLATVYGDTLTPFFTAQSQTYFQTTRGAIDDLFVYCLANDSEFGAHNRTFLNAWTEHYLASSVAALKDFVGLYAKVEKVAGATDSAGVSEALQRVFGDWKIDYADKIGFRVDVDQKVDAVLAGYKN

Entity 2 polymer

描述 description	METHANE MONOOXYGENASE HYDROXYLASE
分子量 formula_weight	59513.7 kDa
EC 编号 ec_number	1.14.13.25
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

MAISLATKAATNRAPVGVEPQEVHKWLQSFNWDFKENRTKYPTKYHMANETKEQFKVIAKEYARMEAAKDERQFGTLLDGLTRLGAGNKVHPRWGETMKVISNFLEVGEYNAIAASAMLWDSATAAEQKNGYLAQVLDEIRHTHQCAFINHYYSKHYHDPAGHNDARRTRAIGPLWKGMKRVFADGFISGDAVECSVNLQLVGEACFTNPLIVAVTEWASANGDEITPTVFLSVETDELRHMANGYQTVVSIANDPASAKFLNTDLNNAFWTQQKYFTPVLGYLFEYGSKFKVEPWVKTWNRWVSEDWGGIWIGRLGKYGVESPRSLRDAKRDAYWAHHDLALAAYAMWPLGFARLALPDEEDQAWFEANYPGWADHYGKIFNEWKKLGYEDPKSGFIPYQWLLANGHDVYIDRVSQVPFIPSLAKGTGSLRVHEFNGKKHSLTDDWGERQWLIEPERYECHNVFEQYEGRELSEVIAEGHGVRSDGKTLIAQPHTRGDNLWTLEDIKRAGCVFPDPLAKF

Entity 3 polymer

描述 description	METHANE MONOOXYGENASE HYDROXYLASE
分子量 formula_weight	19358.3 kDa
EC 编号 ec_number	1.14.13.25
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G

MAKREPIHDNSIRTEWEAKIAKLTSVDQATKFIQDFRLAYTSPFRKSYDIDVDYQYIERKIEEKLSVLKTEKLPVADLITKATTGEDAAAVEATWIAKIKAAKSKYEAEAIHIEFRQLYKPPVLPVNVFLRTDAALGTVLMEIRNTDYYGTPLEGLRKERGVKVLHLQA

Entity 4 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	4

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1mhzb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.25 — Ferritin-like
超家族 Superfamily superfamily	a.25.1 — Ferritin-like
家族 Family family	a.25.1.2 — Ribonucleotide reductase-like

结构域编号 domain_id	d1mhzd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.25 — Ferritin-like
超家族 Superfamily superfamily	a.25.1 — Ferritin-like
家族 Family family	a.25.1.2 — Ribonucleotide reductase-like

结构域编号 domain_id	d1mhzg_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.23 — Open three-helical up-and-down bundle
超家族 Superfamily superfamily	a.23.3 — Methane monooxygenase hydrolase, gamma subunit
家族 Family family	a.23.3.1 — Methane monooxygenase hydrolase, gamma subunit

CATH v4.4 (4 domains)

结构域编号 domain_id	1mhzB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

结构域编号 domain_id	1mhzD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

结构域编号 domain_id	1mhzG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily	10 — Methane monooxygenase, gamma chain, domain 1

结构域编号 domain_id	1mhzG02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily	30 — Methane monooxygenase, gamma chain, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	293.380 Å
晶胞边长 b length_b	64.010 Å
晶胞边长 c length_c	143.650 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	5.000 Å
R 因子 r_factor	0.1520
R_work r_work	0.1520
R_free r_free	—

fit	/app/data/saxs_computation/mh/1mhz/1mhz.fit
pddf	/app/data/pr_computation/mh/1mhz/1mhz.pr.out
profile	/app/data/saxs_computation/mh/1mhz/1mhz.dat

METHANE MONOOXYGENASE HYDROXYLASE

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)