1ozb

Crystal Structure of SecB complexed with SecA C-terminus

Method: X-RAY DIFFRACTION D_max: 110.2 Å Quality: GOOD

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	1ozb
沉积日期 deposition_date	2003-04-08
结构标题 title	Crystal Structure of SecB complexed with SecA C-terminus
关键词 keywords	ZINC BINDING MOTIF, PROTEIN-PROTEIN COMPLEX, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	34.85 Å
回转半径 Rg (电子) rg_electron	33.71 Å
零角强度 I(0) i0	254162000.00
分子量 molecular_weight	129990.0 kDa
排除体积 excluded_volume	162990 Å³
包络体积 envelope_volume	209880 Å³
水化壳体积 shell_volume	50589 Å³
包络直径 envelope_diameter	113.5 Å
壳层 Rg shell_rg	41.72 Å
包络 Rg envelope_rg	33.99 Å
形状 Rg shape_rg	33.70 Å
总 Rg total_rg	34.35 Å
总原子数 total_atoms	9144
残基数 n_residues	1171
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	110.2 Å
Rg (实空间) rg_real	34.75 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	2.5420e+08
I(0) 误差 (实空间) i0_real_error	3.7290e+06
Rg (倒空间) rg_reciprocal	34.81 Å
I(0) (倒空间) i0_reciprocal	254200000.0000
解质量估计 total_estimate	0.8966
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	39.2 Å
偏度 Skewness skewness	0.229
峰度 Kurtosis kurtosis	-0.528
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	61630000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.869

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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 (3)

Entity 1 polymer

描述 description	Protein-export protein secB
分子量 formula_weight	19146.3 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

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	9144

MSEQKQDVAATEEQQPVLQIQRIYVKDVSFEAPNLPHIFQQEWKPKLGFDLSTETTQVGDDLYEVVLNISVETTLEDSGDVAFICEVKQAGVFTISGLEDVQMAHCLTSQCPNMLFPYARELVSNLVNRGTFPALNLSPVNFDALFVEYMNRQQAENAEEKSEEEQTKH

来源 Source

来源生物 organism	Haemophilus influenzae
NCBI 分类编号 ncbi_taxonomy_id	727
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Preprotein translocase secA subunit
分子量 formula_weight	3034.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I,J

RIGRNEPCPCGSGKKYKHCHGSRVARQ

来源 Source

来源生物 organism	Haemophilus influenzae
NCBI 分类编号 ncbi_taxonomy_id	727
宿主生物 host_organism	Escherichia coli

Entity 3 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	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	d1ozba_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.33 — SecB-like
超家族 Superfamily superfamily	d.33.1 — SecB-like
家族 Family family	d.33.1.1 — Bacterial protein-export protein SecB

结构域编号 domain_id	d1ozbb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.33 — SecB-like
超家族 Superfamily superfamily	d.33.1 — SecB-like
家族 Family family	d.33.1.1 — Bacterial protein-export protein SecB

结构域编号 domain_id	d1ozbc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.33 — SecB-like
超家族 Superfamily superfamily	d.33.1 — SecB-like
家族 Family family	d.33.1.1 — Bacterial protein-export protein SecB

结构域编号 domain_id	d1ozbd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.33 — SecB-like
超家族 Superfamily superfamily	d.33.1 — SecB-like
家族 Family family	d.33.1.1 — Bacterial protein-export protein SecB

结构域编号 domain_id	d1ozbe_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.33 — SecB-like
超家族 Superfamily superfamily	d.33.1 — SecB-like
家族 Family family	d.33.1.1 — Bacterial protein-export protein SecB

结构域编号 domain_id	d1ozbf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.33 — SecB-like
超家族 Superfamily superfamily	d.33.1 — SecB-like
家族 Family family	d.33.1.1 — Bacterial protein-export protein SecB

结构域编号 domain_id	d1ozbg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.33 — SecB-like
超家族 Superfamily superfamily	d.33.1 — SecB-like
家族 Family family	d.33.1.1 — Bacterial protein-export protein SecB

结构域编号 domain_id	d1ozbh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.33 — SecB-like
超家族 Superfamily superfamily	d.33.1 — SecB-like
家族 Family family	d.33.1.1 — Bacterial protein-export protein SecB

结构域编号 domain_id	d1ozbi_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.74 — Sec-C motif
超家族 Superfamily superfamily	g.74.1 — Sec-C motif
家族 Family family	g.74.1.1 — Sec-C motif

结构域编号 domain_id	d1ozbj_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.74 — Sec-C motif
超家族 Superfamily superfamily	g.74.1 — Sec-C motif
家族 Family family	g.74.1.1 — Sec-C motif

CATH v4.4 (8 domains)

结构域编号 domain_id	1ozbA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	420 — Bacterial Protein-export protein SecB
同源超家族 H-superfamily homologous superfamily	10 — SecB-like

结构域编号 domain_id	1ozbB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	420 — Bacterial Protein-export protein SecB
同源超家族 H-superfamily homologous superfamily	10 — SecB-like

结构域编号 domain_id	1ozbC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	420 — Bacterial Protein-export protein SecB
同源超家族 H-superfamily homologous superfamily	10 — SecB-like

结构域编号 domain_id	1ozbD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	420 — Bacterial Protein-export protein SecB
同源超家族 H-superfamily homologous superfamily	10 — SecB-like

结构域编号 domain_id	1ozbE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	420 — Bacterial Protein-export protein SecB
同源超家族 H-superfamily homologous superfamily	10 — SecB-like

结构域编号 domain_id	1ozbF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	420 — Bacterial Protein-export protein SecB
同源超家族 H-superfamily homologous superfamily	10 — SecB-like

结构域编号 domain_id	1ozbG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	420 — Bacterial Protein-export protein SecB
同源超家族 H-superfamily homologous superfamily	10 — SecB-like

结构域编号 domain_id	1ozbH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	420 — Bacterial Protein-export protein SecB
同源超家族 H-superfamily homologous superfamily	10 — SecB-like

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7. 引用文献 (1)

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晶胞边长 a length_a	114.500 Å
晶胞边长 b length_b	114.500 Å
晶胞边长 c length_c	286.100 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	64

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	38.160 Å
R 因子 r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2730

fit	/app/data/saxs_computation/oz/1ozb/1ozb.fit
pddf	/app/data/pr_computation/oz/1ozb/1ozb.pr.out
profile	/app/data/saxs_computation/oz/1ozb/1ozb.dat

Crystal Structure of SecB complexed with SecA C-terminus

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

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)