1mpy

STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PSEUDOMONAS PUTIDA MT-2

Method: X-RAY DIFFRACTION D_max: 101.6 Å Quality: REASONABLE

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	1mpy
沉积日期 deposition_date	1998-10-20
结构标题 title	STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PSEUDOMONAS PUTIDA MT-2
关键词 keywords	CATECHOL 2, 3-DIOXYGENASE, EXTRADIOL DIOXYGENASE, NON HEME IRON DIOXYGENASE, METAPYROCATECHASE, 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	32.75 Å
回转半径 Rg (电子) rg_electron	31.65 Å
零角强度 I(0) i0	312714000.00
分子量 molecular_weight	141020.0 kDa
排除体积 excluded_volume	175490 Å³
包络体积 envelope_volume	205210 Å³
水化壳体积 shell_volume	52035 Å³
包络直径 envelope_diameter	105.9 Å
壳层 Rg shell_rg	40.41 Å
包络 Rg envelope_rg	31.56 Å
形状 Rg shape_rg	31.62 Å
总 Rg total_rg	32.36 Å
总原子数 total_atoms	9932
残基数 n_residues	1228
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	101.6 Å
Rg (实空间) rg_real	32.57 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	3.1270e+08
I(0) 误差 (实空间) i0_real_error	4.2420e+06
Rg (倒空间) rg_reciprocal	32.65 Å
I(0) (倒空间) i0_reciprocal	312700000.0000
解质量估计 total_estimate	0.7025
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	40.2 Å
偏度 Skewness skewness	0.201
峰度 Kurtosis kurtosis	-0.480
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	115800000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.992; Smooth: 0.905

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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 (4)

Entity 1 polymer

描述 description	CATECHOL 2,3-DIOXYGENASE
分子量 formula_weight	35203.8 kDa
EC 编号 ec_number	1.13.11.2
来源方法 src_method	man
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	10044

MNKGVMRPGHVQLRVLDMSKALEHYVELLGLIEMDRDDQGRVYLKAWTEVDKFSLVLREADEPGMDFMGFKVVDEDALRQLERDLMAYGCAVEQLPAGELNSCGRRVRFQAPSGHHFELYADKEYTGKWGLNDVNPEAWPRDLKGMAAVRFDHALMYGDELPATYDLFTKVLGFYLAEQVLDENGTRVAQFLSLSTKAHDVAFIHHPEKGRLHHVSFHLETWEDLLRAADLISMTDTSIDIGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYPDHKPVTWTTDQLGKAIFYHDRILNERFMTVLT

来源 Source

来源生物 organism	Pseudomonas putida
NCBI 分类编号 ncbi_taxonomy_id	303
宿主生物 host_organism	Escherichia coli str. K12 substr. W3110

Entity 2 non-polymer

描述 description	FE (II) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	ACETONE
分子量 formula_weight	58.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	112

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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	d1mpya1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
超家族 Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
家族 Family family	d.32.1.3 — Extradiol dioxygenases

结构域编号 domain_id	d1mpya2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
超家族 Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
家族 Family family	d.32.1.3 — Extradiol dioxygenases

结构域编号 domain_id	d1mpyb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
超家族 Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
家族 Family family	d.32.1.3 — Extradiol dioxygenases

结构域编号 domain_id	d1mpyb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
超家族 Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
家族 Family family	d.32.1.3 — Extradiol dioxygenases

结构域编号 domain_id	d1mpyc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
超家族 Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
家族 Family family	d.32.1.3 — Extradiol dioxygenases

结构域编号 domain_id	d1mpyc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
超家族 Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
家族 Family family	d.32.1.3 — Extradiol dioxygenases

结构域编号 domain_id	d1mpyd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
超家族 Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
家族 Family family	d.32.1.3 — Extradiol dioxygenases

结构域编号 domain_id	d1mpyd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
超家族 Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
家族 Family family	d.32.1.3 — Extradiol dioxygenases

CATH v4.4 (8 domains)

结构域编号 domain_id	1mpyA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

结构域编号 domain_id	1mpyA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

结构域编号 domain_id	1mpyB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

结构域编号 domain_id	1mpyB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

结构域编号 domain_id	1mpyC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

结构域编号 domain_id	1mpyC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

结构域编号 domain_id	1mpyD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

结构域编号 domain_id	1mpyD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

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7. 引用文献 (2)

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晶胞边长 a length_a	264.000 Å
晶胞边长 b length_b	264.000 Å
晶胞边长 c length_c	59.800 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	32

空间群 space_group	P 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2800

fit	/app/data/saxs_computation/mp/1mpy/1mpy.fit
pddf	/app/data/pr_computation/mp/1mpy/1mpy.pr.out
profile	/app/data/saxs_computation/mp/1mpy/1mpy.dat