SAXSdb — 1s3t

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1s3t
沉积日期 deposition_date	2004-01-14
结构标题 title	BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE
关键词 keywords	UREASE, BACILLUS PASTEURII, NICKEL, METALLOENZYME, borate, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	30.03 Å
回转半径 Rg (电子) rg_electron	29.31 Å
零角强度 I(0) i0	118665000.00
分子量 molecular_weight	85076.0 kDa
排除体积 excluded_volume	106020 Å³
包络体积 envelope_volume	127000 Å³
水化壳体积 shell_volume	36555 Å³
包络直径 envelope_diameter	107.8 Å
壳层 Rg shell_rg	36.07 Å
包络 Rg envelope_rg	29.64 Å
形状 Rg shape_rg	29.32 Å
总 Rg total_rg	29.88 Å
总原子数 total_atoms	5970
残基数 n_residues	790
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	103.0 Å
Rg (实空间) rg_real	30.06 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	1.1870e+08
I(0) 误差 (实空间) i0_real_error	1.8690e+06
Rg (倒空间) rg_reciprocal	30.05 Å
I(0) (倒空间) i0_reciprocal	118700000.0000
解质量估计 total_estimate	0.8781
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	35.0 Å
偏度 Skewness skewness	0.380
峰度 Kurtosis kurtosis	-0.273
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	37830000.0000
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: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.965

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (7)

Entity 1 polymer

描述 description	Urease gamma subunit
分子量 formula_weight	11205.0 kDa
EC 编号 ec_number	3.5.1.5
来源方法 src_method	nat
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	6376

MHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS

Entity 2 polymer

描述 description	Urease beta subunit
分子量 formula_weight	13975.5 kDa
EC 编号 ec_number	3.5.1.5
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

MSNNNYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE

Entity 3 polymer

描述 description	Urease alpha subunit
分子量 formula_weight	61646.8 kDa
EC 编号 ec_number	3.5.1.5
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

MKINRQQYAESYGPTVGDEVRLADTDLWIEVEKDYTTYGDEVNFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLKIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTLRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRLKRYVSKYTINPAIAQGIAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF

Entity 4 non-polymer

描述 description	NICKEL (II) ION
分子量 formula_weight	58.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	1

Entity 6 non-polymer

描述 description	BORIC ACID
分子量 formula_weight	61.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	406

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1s3ta_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.8 — Urease, gamma-subunit
超家族 Superfamily superfamily	d.8.1 — Urease, gamma-subunit
家族 Family family	d.8.1.1 — Urease, gamma-subunit

结构域编号 domain_id	d1s3tb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.85 — beta-clip
超家族 Superfamily superfamily	b.85.3 — Urease, beta-subunit
家族 Family family	b.85.3.1 — Urease, beta-subunit

结构域编号 domain_id	d1s3tc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.1 — alpha-Subunit of urease

结构域编号 domain_id	d1s3tc2
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.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.2 — alpha-subunit of urease, catalytic domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1s3tA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	280 — Urease; subunit A
同源超家族 H-superfamily homologous superfamily	10 — Urease, gamma-like subunit

结构域编号 domain_id	1s3tB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	150 — Urease, subunit B
同源超家族 H-superfamily homologous superfamily	10 — Urease, beta subunit

结构域编号 domain_id	1s3tC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	1s3tC02
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	140 — Metal-dependent hydrolases

▶

7. 引用文献 (6)

Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism.

J.Am.Chem.Soc. (2004)

PMID: 15038715 · DOI: 10.1021/ja049618p PRIMARY

Structure-Based Rationalization of Urease Inhibition by Phosphate: Novel Insights Into the Enzyme Mechanism

J.Biol.Inorg.Chem. (2001)

DOI: 10.1007/s007750100254

The Complex of Bacillus Pasteurii Urease with Acetohydroxamate Anion from X-Ray Data at 1.55 A Resolution

J.Biol.Inorg.Chem. (2000)

DOI: 10.1007/s007750050014

;A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme from Bacillus Pasteurii: Why Urea Hydrolysis Costs Two Nickels ;

Structure (1999)

DOI: 10.1016/S0969-2126(99)80026-4

The Complex of Bacillus Pasteurii Urease with Beta-Mercaptoethanol from X-Ray Data at 1.65 A Resolution

J.Biol.Inorg.Chem. (1998)

DOI: 10.1007/s007750050231

;Crystallization and Preliminary High-Resolution X-Ray Diffraction Analysis of Native and Beta-Mercaptoethanol-Inhibited Urease from Bacillus Pasteurii ;

Acta Crystallogr.,Sect.D (1998)

DOI: 10.1107/S0907444997013085

▶

晶胞边长 a length_a	130.906 Å
晶胞边长 b length_b	130.906 Å
晶胞边长 c length_c	189.366 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 63 2 2
空间群编号 int_tables_number	182
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	24.770 Å
R 因子 r_factor	0.1781
R_work r_work	0.1775
R_free r_free	0.2046

fit	/app/data/saxs_computation/s3/1s3t/1s3t.fit
pddf	/app/data/pr_computation/s3/1s3t/1s3t.pr.out
profile	/app/data/saxs_computation/s3/1s3t/1s3t.dat

BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE

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

5. 实体与聚合体信息 (7)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)