SAXSdb — 2d3m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2d3m
沉积日期 deposition_date	2005-09-29
结构标题 title	Pentaketide chromone synthase complexed with coenzyme A
关键词 keywords	pentaketide chromone synthase, chalcone synthase, polyketide synthase, TRANSFERASE; TRANSFERASE
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	27.09 Å
回转半径 Rg (电子) rg_electron	26.06 Å
零角强度 I(0) i0	129042000.00
分子量 molecular_weight	89938.0 kDa
排除体积 excluded_volume	112620 Å³
包络体积 envelope_volume	126230 Å³
水化壳体积 shell_volume	38407 Å³
包络直径 envelope_diameter	87.4 Å
壳层 Rg shell_rg	35.21 Å
包络 Rg envelope_rg	26.50 Å
形状 Rg shape_rg	26.08 Å
总 Rg total_rg	26.87 Å
总原子数 total_atoms	6297
残基数 n_residues	798
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	83.2 Å
Rg (实空间) rg_real	26.95 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.2900e+08
I(0) 误差 (实空间) i0_real_error	1.7250e+06
Rg (倒空间) rg_reciprocal	27.00 Å
I(0) (倒空间) i0_reciprocal	129000000.0000
解质量估计 total_estimate	0.9040
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.4 Å
偏度 Skewness skewness	0.219
峰度 Kurtosis kurtosis	-0.454
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	50100000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.952

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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 (3)

Entity 1 polymer

描述 description	pentaketide chromone synthase
分子量 formula_weight	44865.7 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,B
原子数 atom_count	6959

GPGMSSLSNSLPLMEDVQGIRKAQKADGTATVMAIGTAHPPHIFPQDTYADVYFRATNSEHKVELKKKFDHICKKTMIGKRYFNYDEEFLKKYPNITSYDEPSLNDRQDICVPGVPALGTEAAVKAIEEWGRPKSEITHLVFCTSCGVDMPSADFQCAKLLGLHANVNKYCIYMQGCYAGGTVMRYAKDLAENNRGARVLVVCAELTIMMLRAPNETHLDNAIGISLFGDGAAALIIGSDPIIGVEKPMFEIVCTKQTVIPNTEDVIHLHLRETGMMFYLSKGSPMTISNNVEACLIDVFKSVGITPPEDWNSLFWIPHPGGRAILDQVEAKLKLRPEKFRAARTVLWDYGNMVSASVGYILDEMRRKSAAKGLETYGEGLEWGVLLGFGPGITVETILLHSLPLM

来源 Source

来源生物 organism	Aloe arborescens
NCBI 分类编号 ncbi_taxonomy_id	45385
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	COENZYME A
分子量 formula_weight	767.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	566

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2d3ma1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.0 — automated matches

结构域编号 domain_id	d2d3ma2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.0 — automated matches

结构域编号 domain_id	d2d3ma3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2d3mb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.0 — automated matches

结构域编号 domain_id	d2d3mb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2d3mA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	2d3mA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	2d3mB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	2d3mB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

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7. 引用文献 (1)

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晶胞边长 a length_a	73.150 Å
晶胞边长 b length_b	88.400 Å
晶胞边长 c length_c	70.040 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.58 °
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	1.600 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.1980
R_free r_free	0.2070

fit	/app/data/saxs_computation/d3/2d3m/2d3m.fit
pddf	/app/data/pr_computation/d3/2d3m/2d3m.pr.out
profile	/app/data/saxs_computation/d3/2d3m/2d3m.dat

Pentaketide chromone synthase complexed with coenzyme A

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution