1n0f

;CRYSTAL STRUCTURE OF A CELL DIVISION AND CELL WALL BIOSYNTHESIS PROTEIN UPF0040 FROM MYCOPLASMA PNEUMONIAE: INDICATION OF A NOVEL FOLD WITH A POSSIBLE NEW CONSERVED SEQUENCE MOTIF ;

Method: X-RAY DIFFRACTION D_max: 117.3 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1n0f
沉积日期 deposition_date	2002-10-13
结构标题 title	;CRYSTAL STRUCTURE OF A CELL DIVISION AND CELL WALL BIOSYNTHESIS PROTEIN UPF0040 FROM MYCOPLASMA PNEUMONIAE: INDICATION OF A NOVEL FOLD WITH A POSSIBLE NEW CONSERVED SEQUENCE MOTIF ;
关键词 keywords	;Cell Division, cell wall biosynthesis protein, Structural Genomics, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, BIOSYNTHETIC PROTEIN ;; BIOSYNTHETIC PROTEIN
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	38.41 Å
回转半径 Rg (电子) rg_electron	37.72 Å
零角强度 I(0) i0	230798000.00
分子量 molecular_weight	127430.0 kDa
排除体积 excluded_volume	161000 Å³
包络体积 envelope_volume	209250 Å³
水化壳体积 shell_volume	44441 Å³
包络直径 envelope_diameter	115.7 Å
壳层 Rg shell_rg	46.26 Å
包络 Rg envelope_rg	36.40 Å
形状 Rg shape_rg	37.66 Å
总 Rg total_rg	38.44 Å
总原子数 total_atoms	9000
残基数 n_residues	1102
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	117.3 Å
Rg (实空间) rg_real	38.22 Å
Rg 误差 (实空间) rg_real_error	0.89 Å
I(0) (实空间) i0_real	2.3080e+08
I(0) 误差 (实空间) i0_real_error	3.9220e+06
Rg (倒空间) rg_reciprocal	38.35 Å
I(0) (倒空间) i0_reciprocal	230800000.0000
解质量估计 total_estimate	0.9022
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	60.1 Å
偏度 Skewness skewness	0.005
峰度 Kurtosis kurtosis	-0.845
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	52330000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.975

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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 (2)

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1n0fa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.129 — Double-split beta-barrel
超家族 Superfamily superfamily	b.129.1 — AbrB/MazE/MraZ-like
家族 Family family	b.129.1.2 — Hypothetical protein MraZ

结构域编号 domain_id	d1n0fa2
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	d1n0fb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.129 — Double-split beta-barrel
超家族 Superfamily superfamily	b.129.1 — AbrB/MazE/MraZ-like
家族 Family family	b.129.1.2 — Hypothetical protein MraZ

结构域编号 domain_id	d1n0fb2
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	d1n0fc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.129 — Double-split beta-barrel
超家族 Superfamily superfamily	b.129.1 — AbrB/MazE/MraZ-like
家族 Family family	b.129.1.2 — Hypothetical protein MraZ

结构域编号 domain_id	d1n0fd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.129 — Double-split beta-barrel
超家族 Superfamily superfamily	b.129.1 — AbrB/MazE/MraZ-like
家族 Family family	b.129.1.2 — Hypothetical protein MraZ

结构域编号 domain_id	d1n0fe_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.129 — Double-split beta-barrel
超家族 Superfamily superfamily	b.129.1 — AbrB/MazE/MraZ-like
家族 Family family	b.129.1.2 — Hypothetical protein MraZ

结构域编号 domain_id	d1n0ff_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.129 — Double-split beta-barrel
超家族 Superfamily superfamily	b.129.1 — AbrB/MazE/MraZ-like
家族 Family family	b.129.1.2 — Hypothetical protein MraZ

结构域编号 domain_id	d1n0fg_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.129 — Double-split beta-barrel
超家族 Superfamily superfamily	b.129.1 — AbrB/MazE/MraZ-like
家族 Family family	b.129.1.2 — Hypothetical protein MraZ

结构域编号 domain_id	d1n0fh_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.129 — Double-split beta-barrel
超家族 Superfamily superfamily	b.129.1 — AbrB/MazE/MraZ-like
家族 Family family	b.129.1.2 — Hypothetical protein MraZ

CATH v4.4 (8 domains)

结构域编号 domain_id	1n0fA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1550 — Chemotaxis protein chec
同源超家族 H-superfamily homologous superfamily	20 — Transcriptional regulator MraZ domain

结构域编号 domain_id	1n0fB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1550 — Chemotaxis protein chec
同源超家族 H-superfamily homologous superfamily	20 — Transcriptional regulator MraZ domain

结构域编号 domain_id	1n0fC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1550 — Chemotaxis protein chec
同源超家族 H-superfamily homologous superfamily	20 — Transcriptional regulator MraZ domain

结构域编号 domain_id	1n0fD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1550 — Chemotaxis protein chec
同源超家族 H-superfamily homologous superfamily	20 — Transcriptional regulator MraZ domain

结构域编号 domain_id	1n0fE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1550 — Chemotaxis protein chec
同源超家族 H-superfamily homologous superfamily	20 — Transcriptional regulator MraZ domain

结构域编号 domain_id	1n0fF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1550 — Chemotaxis protein chec
同源超家族 H-superfamily homologous superfamily	20 — Transcriptional regulator MraZ domain

结构域编号 domain_id	1n0fG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1550 — Chemotaxis protein chec
同源超家族 H-superfamily homologous superfamily	20 — Transcriptional regulator MraZ domain

结构域编号 domain_id	1n0fH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1550 — Chemotaxis protein chec
同源超家族 H-superfamily homologous superfamily	20 — Transcriptional regulator MraZ domain

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7. 引用文献 (1)

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晶胞边长 a length_a	84.893 Å
晶胞边长 b length_b	101.180 Å
晶胞边长 c length_c	169.046 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	32

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	2.800 Å
最低分辨率 resolution_low	13.010 Å
R 因子 r_factor	0.2400
R_work r_work	0.2400
R_free r_free	0.2840

描述 description	Protein mraZ
分子量 formula_weight	19342.9 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	9184

;CRYSTAL STRUCTURE OF A CELL DIVISION AND CELL WALL BIOSYNTHESIS PROTEIN UPF0040 FROM MYCOPLASMA PNEUMONIAE: INDICATION OF A NOVEL FOLD WITH A POSSIBLE NEW CONSERVED SEQUENCE MOTIF ;

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Mycoplasma pneumoniae
NCBI 分类编号 ncbi_taxonomy_id	2104
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	184

fit	/app/data/saxs_computation/n0/1n0f/1n0f.fit
pddf	/app/data/pr_computation/n0/1n0f/1n0f.pr.out
profile	/app/data/saxs_computation/n0/1n0f/1n0f.dat