2iah

Crystal structure of the ferripyoverdine receptor of the outer membrane of Pseudomonas aeruginosa bound to ferripyoverdine.

Method: X-RAY DIFFRACTION D_max: 104.6 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	2iah
沉积日期 deposition_date	2006-09-08
结构标题 title	Crystal structure of the ferripyoverdine receptor of the outer membrane of Pseudomonas aeruginosa bound to ferripyoverdine.
关键词 keywords	PYOVERDINE, FPVA, TONB BOX, SIDEROPHORE, CELL MEMBRANE, ION TRANSPORT, TONB DEPENDENT RECEPTOR, MEMBRANE PROTEIN; MEMBRANE 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	28.43 Å
回转半径 Rg (电子) rg_electron	27.93 Å
零角强度 I(0) i0	121728000.00
分子量 molecular_weight	84912.0 kDa
排除体积 excluded_volume	105040 Å³
包络体积 envelope_volume	133690 Å³
水化壳体积 shell_volume	39523 Å³
包络直径 envelope_diameter	111.1 Å
壳层 Rg shell_rg	35.79 Å
包络 Rg envelope_rg	28.29 Å
形状 Rg shape_rg	27.94 Å
总 Rg total_rg	28.62 Å
总原子数 total_atoms	6005
残基数 n_residues	756
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	104.6 Å
Rg (实空间) rg_real	28.47 Å
Rg 误差 (实空间) rg_real_error	0.89 Å
I(0) (实空间) i0_real	1.2170e+08
I(0) 误差 (实空间) i0_real_error	1.8970e+06
Rg (倒空间) rg_reciprocal	28.46 Å
I(0) (倒空间) i0_reciprocal	121700000.0000
解质量估计 total_estimate	0.8156
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	35.5 Å
偏度 Skewness skewness	0.516
峰度 Kurtosis kurtosis	0.258
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30530000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.560; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.968

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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	Ferripyoverdine receptor
分子量 formula_weight	86556.1 kDa
来源方法 src_method	man
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	6005

QEVEFDIPPQALGSALQEFGRQADIQVLYRPEEVRNKRSSAIKGKLEPNQAITELLRGTGASVDFQGNAITISVAEAADSSVDLGATMITSNQLGTITEDSGSYTPGTIATATRLVLTPRETPQSITVVTRQNMDDFGLNNIDDVMRHTPGITVSAYDTDRNNYYARGFSINNFQYDGIPSTARNVGYSAGNTLSDMAIYDRVEVLKGATGLLTGAGSLGATINLIRKKPTHEFKGHVELGAGSWDNYRSELDVSGPLTESGNVRGRAVAAYQDKHSFMDHYERKTSVYYGILEFDLNPDTMLTVGADYQDNDPKGSGWSGSFPLFDSQGNRNDVSRSFNNGAKWSSWEQYTRTVFANLEHNFANGWVGKVQLDHKINGYHAPLGAIMGDWPAPDNSAKIVAQKYTGETKSNSLDIYLTGPFQFLGREHELVVGTSASFSHWEGKSYWNLRNYDNTTDDFINWDGDIGKPDWGTPSQYIDDKTRQLGSYMTARFNVTDDLNLFLGGRVVDYRVTGLNPTIRESGRFIPYVGAVYDLNDTYSVYASYTDIFMPQDSWYRDSSNKLLEPDEGQNYEIGIKGEYLDGRLNTSLAYFEIHEENRAEEDALYNSKPTNPAITYAYKGIKAKTKGYEAEISGELAPGWQVQAGYTHKIIRDDSGKKVSTWEPQDQLSLYTSYKFKGALDKLTVGGGARWQGKSWQMVYNNPRSRWEKFSQEDYWLVDLMARYQITDKLSASVNVNNVFDKTYYTNIGFYTSASYGDPRNLMFSTRWDF

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	Pseudomonas aeruginosa

Entity 2 polymer

描述 description	Pyoverdin C-E
分子量 formula_weight	997.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

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

SRSKKKTT

Entity 3 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 4 non-polymer

描述 description	(1S)-1-CARBOXY-5-[(3-CARBOXYPROPANOYL)AMINO]-8,9-DIHYDROXY-1,2,3,4-TETRAHYDROPYRIMIDO[1,2-A]QUINOLIN-11-IUM
分子量 formula_weight	376.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	1

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	2iahA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	55 — 3-Layer(bab) Sandwich
拓扑 Topology topology	50 — Phage tail protein beta-alpha-beta fold
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	2iahA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — TonB-dependent receptor, plug domain

结构域编号 domain_id	2iahA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	170 — Maltoporin; Chain A
同源超家族 H-superfamily homologous superfamily	20 — TonB-dependent receptor, beta-barrel domain

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7. 引用文献 (1)

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晶胞边长 a length_a	82.123 Å
晶胞边长 b length_b	82.123 Å
晶胞边长 c length_c	286.225 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	8

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	2.730 Å
最低分辨率 resolution_low	46.960 Å
R 因子 r_factor	0.2461
R_work r_work	0.2441
R_free r_free	0.2852

fit	/app/data/saxs_computation/ia/2iah/2iah.fit
pddf	/app/data/pr_computation/ia/2iah/2iah.pr.out
profile	/app/data/saxs_computation/ia/2iah/2iah.dat

Crystal structure of the ferripyoverdine receptor of the outer membrane of Pseudomonas aeruginosa bound to ferripyoverdine.

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)