SAXSdb — 1mmd

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mmd
沉积日期 deposition_date	1995-03-21
结构标题 title	TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM DISCOIDEUM COMPLEXED WITH MGADP-BEF3
关键词 keywords	;ATPASE, MYOSIN, COILED COIL, ACTIN-BINDING, ATP-BINDING, HEPTAD REPEAT PATTERN, METHYLATION, ALKYLATION, PHOSPHORYLATION, CONTRACTILE PROTEIN ;; CONTRACTILE 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	30.12 Å
回转半径 Rg (电子) rg_electron	29.51 Å
零角强度 I(0) i0	111822000.00
分子量 molecular_weight	83729.0 kDa
排除体积 excluded_volume	104800 Å³
包络体积 envelope_volume	132690 Å³
水化壳体积 shell_volume	37784 Å³
包络直径 envelope_diameter	108.2 Å
壳层 Rg shell_rg	36.40 Å
包络 Rg envelope_rg	29.79 Å
形状 Rg shape_rg	29.51 Å
总 Rg total_rg	30.14 Å
总原子数 total_atoms	5908
残基数 n_residues	743
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	102.4 Å
Rg (实空间) rg_real	30.18 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	1.1180e+08
I(0) 误差 (实空间) i0_real_error	1.6260e+06
Rg (倒空间) rg_reciprocal	30.16 Å
I(0) (倒空间) i0_reciprocal	111800000.0000
解质量估计 total_estimate	0.8674
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	34.8 Å
偏度 Skewness skewness	0.472
峰度 Kurtosis kurtosis	-0.099
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21840000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.931

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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	MYOSIN
分子量 formula_weight	86749.0 kDa
EC 编号 ec_number	3.6.1.32
突变 mutation	Q760L, R761P, I762N
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6283

MNPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPDERDSYECGEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQFNNAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDEDEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCSERAAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQFFNHHMFKVEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEARELPN

来源 Source

来源生物 organism	Dictyostelium discoideum
NCBI 分类编号 ncbi_taxonomy_id	44689
宿主生物 host_organism	Dictyostelium discoideum

Entity 2 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	1

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	BERYLLIUM TRIFLUORIDE ION
分子量 formula_weight	66.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	375

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1mmda1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.3 — Myosin S1 fragment, N-terminal domain
家族 Family family	b.34.3.1 — Myosin S1 fragment, N-terminal domain

结构域编号 domain_id	d1mmda2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.9 — Motor proteins

CATH v4.4 (6 domains)

结构域编号 domain_id	1mmdA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	360 — Myosin S1 fragment, N-terminal

结构域编号 domain_id	1mmdA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	850 — Kinesin
同源超家族 H-superfamily homologous superfamily	10 — Kinesin motor domain

结构域编号 domain_id	1mmdA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	820 —

结构域编号 domain_id	1mmdA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	720 — Myosin VI head, motor domain, U50 subdomain

结构域编号 domain_id	1mmdA05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	530 —

结构域编号 domain_id	1mmdA06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1590 —

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7. 引用文献 (3)

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晶胞边长 a length_a	105.300 Å
晶胞边长 b length_b	182.600 Å
晶胞边长 c length_c	54.700 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	4

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/mm/1mmd/1mmd.fit
pddf	/app/data/pr_computation/mm/1mmd/1mmd.pr.out
profile	/app/data/saxs_computation/mm/1mmd/1mmd.dat

TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM DISCOIDEUM COMPLEXED WITH MGADP-BEF3

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution