SAXSdb — 1q3k

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1q3k
沉积日期 deposition_date	2003-07-30
结构标题 title	Crystal structure of creatinine amidohydrolase (creatininase)
关键词 keywords	alpha-beta-fold, HYDROLASE; HYDROLASE
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	33.80 Å
回转半径 Rg (电子) rg_electron	32.95 Å
零角强度 I(0) i0	436484000.00
分子量 molecular_weight	171380.0 kDa
排除体积 excluded_volume	215170 Å³
包络体积 envelope_volume	250150 Å³
水化壳体积 shell_volume	59532 Å³
包络直径 envelope_diameter	103.1 Å
壳层 Rg shell_rg	42.45 Å
包络 Rg envelope_rg	32.96 Å
形状 Rg shape_rg	32.95 Å
总 Rg total_rg	33.60 Å
总原子数 total_atoms	12036
残基数 n_residues	1554
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	103.2 Å
Rg (实空间) rg_real	33.62 Å
Rg 误差 (实空间) rg_real_error	0.68 Å
I(0) (实空间) i0_real	4.3650e+08
I(0) 误差 (实空间) i0_real_error	6.5870e+06
Rg (倒空间) rg_reciprocal	33.73 Å
I(0) (倒空间) i0_reciprocal	436500000.0000
解质量估计 total_estimate	0.8998
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	41.7 Å
偏度 Skewness skewness	0.139
峰度 Kurtosis kurtosis	-0.514
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	61940000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.934

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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	creatininase
分子量 formula_weight	28428.5 kDa
EC 编号 ec_number	3.5.2.10
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	12760

SKSVFVGELTWKEYEARVAAGDCVLMLPVGALEQHGHHMCMNVDVLLPTAVCQRVAERIGALVLPGLQYGYKSQQKSGGGNHFPGTTSLDGATLTGTVQDIIRELARHGVRRLVLMNGHYENSMFIVEGIDLALRELRYAGIHDFKVVVLSYWDFVKDPAVIQRLYPEGFLGWDIEHGGVFETSLMLALYPDLVDLERVVDHPPATFPPYDVFPVDPARTPAPGTLSSAKTASREKGELILEVCVQGIADAIGQEFPPT

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

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 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	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	724

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1q3ka_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.125 — Creatininase
超家族 Superfamily superfamily	c.125.1 — Creatininase
家族 Family family	c.125.1.1 — Creatininase

结构域编号 domain_id	d1q3kb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.125 — Creatininase
超家族 Superfamily superfamily	c.125.1 — Creatininase
家族 Family family	c.125.1.1 — Creatininase

结构域编号 domain_id	d1q3kc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.125 — Creatininase
超家族 Superfamily superfamily	c.125.1 — Creatininase
家族 Family family	c.125.1.1 — Creatininase

结构域编号 domain_id	d1q3kd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.125 — Creatininase
超家族 Superfamily superfamily	c.125.1 — Creatininase
家族 Family family	c.125.1.1 — Creatininase

结构域编号 domain_id	d1q3ke_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.125 — Creatininase
超家族 Superfamily superfamily	c.125.1 — Creatininase
家族 Family family	c.125.1.1 — Creatininase

结构域编号 domain_id	d1q3kf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.125 — Creatininase
超家族 Superfamily superfamily	c.125.1 — Creatininase
家族 Family family	c.125.1.1 — Creatininase

CATH v4.4 (6 domains)

结构域编号 domain_id	1q3kA00
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	10310 — Creatininase

结构域编号 domain_id	1q3kB00
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	10310 — Creatininase

结构域编号 domain_id	1q3kC00
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	10310 — Creatininase

结构域编号 domain_id	1q3kD00
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	10310 — Creatininase

结构域编号 domain_id	1q3kE00
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	10310 — Creatininase

结构域编号 domain_id	1q3kF00
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	10310 — Creatininase

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7. 引用文献 (1)

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晶胞边长 a length_a	74.392 Å
晶胞边长 b length_b	94.084 Å
晶胞边长 c length_c	114.746 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.62 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	2.100 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2090
R_work r_work	0.2070
R_free r_free	0.2470

fit	/app/data/saxs_computation/q3/1q3k/1q3k.fit
pddf	/app/data/pr_computation/q3/1q3k/1q3k.pr.out
profile	/app/data/saxs_computation/q3/1q3k/1q3k.dat

Crystal structure of creatinine amidohydrolase (creatininase)

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