SAXSdb — 1nx4

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nx4
沉积日期 deposition_date	2003-02-08
结构标题 title	The crystal structure of carbapenem synthase (CarC)
关键词 keywords	jelly roll, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	30.38 Å
回转半径 Rg (电子) rg_electron	29.36 Å
零角强度 I(0) i0	121235000.00
分子量 molecular_weight	87053.0 kDa
排除体积 excluded_volume	108390 Å³
包络体积 envelope_volume	136890 Å³
水化壳体积 shell_volume	37797 Å³
包络直径 envelope_diameter	97.4 Å
壳层 Rg shell_rg	37.57 Å
包络 Rg envelope_rg	29.22 Å
形状 Rg shape_rg	29.38 Å
总 Rg total_rg	30.02 Å
总原子数 total_atoms	6105
残基数 n_residues	738
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	88.6 Å
Rg (实空间) rg_real	30.23 Å
Rg 误差 (实空间) rg_real_error	0.51 Å
I(0) (实空间) i0_real	1.2120e+08
I(0) 误差 (实空间) i0_real_error	1.8450e+06
Rg (倒空间) rg_reciprocal	30.30 Å
I(0) (倒空间) i0_reciprocal	121200000.0000
解质量估计 total_estimate	0.9085
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	86.9 Å
偏度 Skewness skewness	0.088
峰度 Kurtosis kurtosis	-0.726
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	49600000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.989; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.840

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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	Carbapenem synthase
分子量 formula_weight	31931.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	6348

MSEIVKFNPVMASGFGAYIDHRDFLEAKTETIKNLLMRQGFVVVKNLDIDSDTFRDIYSAYGTIVEYADEKIGVGFGYRDTLKLEGEKGKIVTGRGQLPFHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEMPAHLLRVLEEETFEVRVLERGYYVDVSPDGWFKVPVFTDLGWVRKMLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYYYKHFWEDGDLLIMDNRRVIHEREEFNDDDIVRRLYRGQTADI

来源 Source

来源生物 organism	Pectobacterium carotovorum
NCBI 分类编号 ncbi_taxonomy_id	554
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	2-OXOGLUTARIC ACID
分子量 formula_weight	146.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	243

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1nx4a_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.2 — Clavaminate synthase-like
家族 Family family	b.82.2.8 — gamma-Butyrobetaine hydroxylase

结构域编号 domain_id	d1nx4b_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.2 — Clavaminate synthase-like
家族 Family family	b.82.2.8 — gamma-Butyrobetaine hydroxylase

结构域编号 domain_id	d1nx4c_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.2 — Clavaminate synthase-like
家族 Family family	b.82.2.8 — gamma-Butyrobetaine hydroxylase

CATH v4.4 (3 domains)

结构域编号 domain_id	1nx4A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	130 — Double-stranded beta-helix
同源超家族 H-superfamily homologous superfamily	10 — Clavaminate synthase-like

结构域编号 domain_id	1nx4B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	130 — Double-stranded beta-helix
同源超家族 H-superfamily homologous superfamily	10 — Clavaminate synthase-like

结构域编号 domain_id	1nx4C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	130 — Double-stranded beta-helix
同源超家族 H-superfamily homologous superfamily	10 — Clavaminate synthase-like

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7. 引用文献 (6)

Crystal structure of carbapenem synthase (CarC).

J.Biol.Chem. (2003)

PMID: 12611886 · DOI: 10.1074/jbc.M213054200 PRIMARY

;Diastereoselective synthesis of 3,5-trans-(+)-(3R,5R)-3- carbomethoxycarbapenam from 3-hydroxypyridine: questioning the stereochemical assignment of the natural product ;

TETRAHEDRON LETT. (2002)

DOI: 10.1016/S0040-4039(01)02073-1

Three Unusual Reactions Mediate Carbapenem and Carbapenam Biosynthesis

J.AM.CHEM.SOC. (2000)

DOI: 10.1021/ja001723l

Bacterial production of carbapenems and clavams: evolution of beta-lactam antibiotic pathways

Trends Microbiol. (1998)

DOI: 10.1016/S0966-842X(98)01251-7

;Analysis of the carbapenem gene cluster of Erwinia carotovora: definition of the antibiotic biosynthetic genes and evidence for a novel beta-lactam resistance mechanism ;

MOL.MICROBIOL. (1997)

DOI: 10.1046/j.1365-2958.1997.6001974.x

;A Chiral Synthesis of trans-Carbapenam-3-carboxylic Acid and the Assignment of (3S, 5S) Configuration to the Corresponding Product from Serratia and Erwinia Species. ;

J.CHEM.SOC.,CHEM.COMMUN. (1989)

DOI: 10.1039/c39890000423

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晶胞边长 a length_a	79.930 Å
晶胞边长 b length_b	163.946 Å
晶胞边长 c length_c	146.455 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	81.650 Å
R 因子 r_factor	0.2232
R_work r_work	0.2208
R_free r_free	0.2678

fit	/app/data/saxs_computation/nx/1nx4/1nx4.fit
pddf	/app/data/pr_computation/nx/1nx4/1nx4.pr.out
profile	/app/data/saxs_computation/nx/1nx4/1nx4.dat

The crystal structure of carbapenem synthase (CarC)

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