1req

METHYLMALONYL-COA MUTASE

Method: X-RAY DIFFRACTION D_max: 173.4 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	1req
沉积日期 deposition_date	1996-01-19
结构标题 title	METHYLMALONYL-COA MUTASE
关键词 keywords	ISOMERASE, MUTASE, INTRAMOLECULAR TRANSFERASE; ISOMERASE
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	55.52 Å
回转半径 Rg (电子) rg_electron	55.79 Å
零角强度 I(0) i0	1259250000.00
分子量 molecular_weight	295980.0 kDa
排除体积 excluded_volume	369560 Å³
包络体积 envelope_volume	491370 Å³
水化壳体积 shell_volume	73401 Å³
包络直径 envelope_diameter	186.3 Å
壳层 Rg shell_rg	58.23 Å
包络 Rg envelope_rg	54.49 Å
形状 Rg shape_rg	55.76 Å
总 Rg total_rg	55.96 Å
总原子数 total_atoms	20840
残基数 n_residues	2695
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	173.4 Å
Rg (实空间) rg_real	55.85 Å
Rg 误差 (实空间) rg_real_error	1.95 Å
I(0) (实空间) i0_real	1.2590e+09
I(0) 误差 (实空间) i0_real_error	2.5900e+07
Rg (倒空间) rg_reciprocal	55.19 Å
I(0) (倒空间) i0_reciprocal	1258000000.0000
解质量估计 total_estimate	0.5787
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	43.4 Å
偏度 Skewness skewness	0.372
峰度 Kurtosis kurtosis	-0.760
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	95890000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 0.041; Positv: 1.000; Valcen: 0.885; Smooth: 0.018

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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	METHYLMALONYL-COA MUTASE
分子量 formula_weight	80137.9 kDa
EC 编号 ec_number	5.4.99.2
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	22372

STLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASLDA

来源 Source

来源生物 organism	Propionibacterium freudenreichii subsp. shermanii
NCBI 分类编号 ncbi_taxonomy_id	1752
宿主生物 host_organism	K38 PGP1-2

Entity 2 polymer

描述 description	METHYLMALONYL-COA MUTASE
分子量 formula_weight	69430.2 kDa
EC 编号 ec_number	5.4.99.2
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

SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKRLTVHTVDGIDIVPMYRPKDAPKKLGYPGVAPFTRGTTVRNGDMDAWDVRALHEDPDEKFTRKAILEGLERGVTSLLLRVDPDAIAPEHLDEVLSDVLLEMTKVEVFSRYDQGAAAEALVSVYERSDKPAKDLALNLGLDPIGFAALQGTEPDLTVLGDWVRRLAKFSPDSRAVTIDANIYHNAGAGDVAELAWALATGAEYVRALVEQGFTATEAFDTINFRVTATHDQFLTIARLRALREAWARIGEVFGVDEDKRGARQNAITSWRELTREDPYVNILRGSIATFSASVGGAESITTLPFTQALGLPEDDFPLRIARNTGIVLAEEVNIGRVNDPAGGSYYVESLTRSLADAAWKEFQEVEKLGGMSKAVMTEHVTKVLDACNAERAKRLANRKQPITAVSEFPMIGARSIETKPFPAAPARKGLAWHRDSEVFEQLMDRSTSVSERPKVFLACLGTRRDFGGREGFSSPVWHIAGIDTPQVEGGTTAEIVEAFKKSGAQVADLCSSAKVYAQQGLEVAKALKAAGAKALYLSGAFKEFGDDAAEAEKLIDGRLFMGMDVVDTLSSTLDILGVAK

来源 Source

来源生物 organism	Propionibacterium freudenreichii subsp. shermanii
NCBI 分类编号 ncbi_taxonomy_id	1752
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	COBALAMIN
分子量 formula_weight	1330.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	DESULFO-COENZYME A
分子量 formula_weight	735.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

Entity 6 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	1532

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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	d1reqa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
家族 Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

结构域编号 domain_id	d1reqa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
家族 Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

结构域编号 domain_id	d1reqb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
家族 Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

结构域编号 domain_id	d1reqb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
家族 Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

结构域编号 domain_id	d1reqc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
家族 Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

结构域编号 domain_id	d1reqc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
家族 Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

结构域编号 domain_id	d1reqd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
家族 Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

结构域编号 domain_id	d1reqd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
家族 Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1reqA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

结构域编号 domain_id	1reqA02
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	280 — Cobalamin-binding domain

结构域编号 domain_id	1reqB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

结构域编号 domain_id	1reqB02
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	280 — Cobalamin-binding domain

结构域编号 domain_id	1reqC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

结构域编号 domain_id	1reqC02
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	280 — Cobalamin-binding domain

结构域编号 domain_id	1reqD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

结构域编号 domain_id	1reqD02
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	280 — Cobalamin-binding domain

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7. 引用文献 (2)

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晶胞边长 a length_a	119.800 Å
晶胞边长 b length_b	161.300 Å
晶胞边长 c length_c	88.400 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.10 °
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	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2200
R_free r_free	0.2750

fit	/app/data/saxs_computation/re/1req/1req.fit
pddf	/app/data/pr_computation/re/1req/1req.pr.out
profile	/app/data/saxs_computation/re/1req/1req.dat

METHYLMALONYL-COA MUTASE

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 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)