SAXSdb — 1j2t

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1j2t
沉积日期 deposition_date	2003-01-11
结构标题 title	Creatininase Mn
关键词 keywords	creatinine, creatine, 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	34.03 Å
回转半径 Rg (电子) rg_electron	33.14 Å
零角强度 I(0) i0	441804000.00
分子量 molecular_weight	171010.0 kDa
排除体积 excluded_volume	214110 Å³
包络体积 envelope_volume	254590 Å³
水化壳体积 shell_volume	60211 Å³
包络直径 envelope_diameter	106.7 Å
壳层 Rg shell_rg	42.63 Å
包络 Rg envelope_rg	33.17 Å
形状 Rg shape_rg	33.14 Å
总 Rg total_rg	33.79 Å
总原子数 total_atoms	11990
残基数 n_residues	1542
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	102.9 Å
Rg (实空间) rg_real	33.84 Å
Rg 误差 (实空间) rg_real_error	0.41 Å
I(0) (实空间) i0_real	4.4180e+08
I(0) 误差 (实空间) i0_real_error	5.7540e+06
Rg (倒空间) rg_reciprocal	33.96 Å
I(0) (倒空间) i0_reciprocal	441800000.0000
解质量估计 total_estimate	0.8990
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	41.6 Å
偏度 Skewness skewness	0.139
峰度 Kurtosis kurtosis	-0.506
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	66860000.0000
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: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.885

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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	creatinine amidohydrolase
分子量 formula_weight	28598.8 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	13386

MSKSVFVGELTWKEYEARVAAGDCVLMLPVGALEQHGHHMCMNVDVLLPTAVCKRVAERIGALVMPGLQYGYKSQQKSGGGNHFPGTTSLDGATLTGTVQDIIRELARHGARRLVLMNGHYENSMFIVEGIDLALRELRYAGIQDFKVVVLSYWDFVKDPAVIQQLYPEGFLGWDIEHGGVFETSLMLALYPDLVDLDRVVDHPPATFPPYDVFPVDPARTPAPGTLSSAKTASREKGELILEVCVQGIADAIREEFPPT

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	6

Entity 3 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	1396

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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	d1j2ta_
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	d1j2tb_
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	d1j2tc_
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	d1j2td_
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	d1j2te_
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	d1j2tf_
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	1j2tA00
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	1j2tB00
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	1j2tC00
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	1j2tD00
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	1j2tE00
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	1j2tF00
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	101.989 Å
晶胞边长 b length_b	150.742 Å
晶胞边长 c length_c	167.066 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	24

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.1759
R_work r_work	0.1750
R_free r_free	0.1932

fit	/app/data/saxs_computation/j2/1j2t/1j2t.fit
pddf	/app/data/pr_computation/j2/1j2t/1j2t.pr.out
profile	/app/data/saxs_computation/j2/1j2t/1j2t.dat

Creatininase Mn

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