2grx

Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for ferrichrome

Method: X-RAY DIFFRACTION D_max: 125.7 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	2grx
沉积日期 deposition_date	2006-04-25
结构标题 title	Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for ferrichrome
关键词 keywords	BETA BARREL, OUTER MEMBRANE, HETEROCOMPLEX, INTER-PROTEIN BETA SHEET, PROTEIN-PROTEIN, METAL TRANSPORT; METAL 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	39.84 Å
回转半径 Rg (电子) rg_electron	39.56 Å
零角强度 I(0) i0	483940000.00
分子量 molecular_weight	177740.0 kDa
排除体积 excluded_volume	221070 Å³
包络体积 envelope_volume	287660 Å³
水化壳体积 shell_volume	59477 Å³
包络直径 envelope_diameter	131.1 Å
壳层 Rg shell_rg	46.06 Å
包络 Rg envelope_rg	39.41 Å
形状 Rg shape_rg	39.58 Å
总 Rg total_rg	39.84 Å
总原子数 total_atoms	12533
残基数 n_residues	1549
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	125.7 Å
Rg (实空间) rg_real	39.80 Å
Rg 误差 (实空间) rg_real_error	0.82 Å
I(0) (实空间) i0_real	4.8390e+08
I(0) 误差 (实空间) i0_real_error	8.5400e+06
Rg (倒空间) rg_reciprocal	39.83 Å
I(0) (倒空间) i0_reciprocal	484000000.0000
解质量估计 total_estimate	0.8928
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	37.7 Å
偏度 Skewness skewness	0.238
峰度 Kurtosis kurtosis	-0.669
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	138100000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.802

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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 (10)

Entity 1 polymer

描述 description	Ferrichrome-iron receptor
分子量 formula_weight	80051.1 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	A,B
原子数 atom_count	12533

AVEPKEDTITVTAAPAPQESAWGPAATIAARQSATGTKTDTPIQKVPQSISVVTAEEMALHQPKSVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAVIDPYMLERAEIMRGPVSVLYGKSSPGGLLNMVSKRPTTEPLKEVQFKAGTDSLFQTGFDFSDSLDDDGVYSYRLTGLARSANAQQKGSEEQRYAIAPAFTWRPDDKTNFTFLSYFQNEPETGYYGWLPKEGTVEPLPNGKRLPTDFNEGAKNNTYSRNEKMVGYSFDHEFNDTFTVRQNLRFAENKTSQNSVYGYGVCSDPANAYSKQCAALAPADKGHYLARKYVVDDEKLQNFSVDTQLQSKFATGDIDHTLLTGVDFMRMRNDINAWFGYDDSVPLLNLYNPSSHHHHHHGSSVNTDFDFNAKDPANSGPYRILNKQKQTGVYVQDQAQWDKVLVTLGGRYDWADQESLNRVAGTTDKRDDKQFTWRGGVNYLFDNGVTPYFSYSESFEPSSQVGKDGNIFAPSKGKQYEVGVKYVPEDRPIVVTGAVYNLTKTNNLMADPEGSFFSVEGGEIRARGVEIEAKAALSASVNVVGSYTYTDAEYTTDTTYKGNTPAQVPKHMASLWADYTFFDGPLSGLTLGTGGRYTGSSYGDPANSFKVGSYTVVDALVRYDLARVGMAGSNVALHVNNLFDREYVASCFNTYGCFWGAERQVVATATFRF

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Protein tonB
分子量 formula_weight	24973.6 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	C,D

GSSHHHHHHSSGLVPRGSHMSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQYPARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTEIQ

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 branched

描述 description	;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose-(1-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose ;
分子量 formula_weight	940.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	3-HYDROXY-TETRADECANOIC ACID
分子量 formula_weight	244.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 6 non-polymer

描述 description	DIPHOSPHATE
分子量 formula_weight	173.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	LAURIC ACID
分子量 formula_weight	200.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 non-polymer

描述 description	2-AMINO-VINYL-PHOSPHATE
分子量 formula_weight	139.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	FERRICROCIN-IRON
分子量 formula_weight	770.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 non-polymer

描述 description	MYRISTIC ACID
分子量 formula_weight	228.4 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) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2grxa1
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.4 — Transmembrane beta-barrels
超家族 Superfamily superfamily	f.4.3 — Porins
家族 Family family	f.4.3.3 — Ligand-gated protein channel

结构域编号 domain_id	d2grxb1
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.4 — Transmembrane beta-barrels
超家族 Superfamily superfamily	f.4.3 — Porins
家族 Family family	f.4.3.3 — Ligand-gated protein channel

结构域编号 domain_id	d2grxc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.212 — TolA/TonB C-terminal domain
超家族 Superfamily superfamily	d.212.1 — TolA/TonB C-terminal domain
家族 Family family	d.212.1.2 — TonB

结构域编号 domain_id	d2grxd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.212 — TolA/TonB C-terminal domain
超家族 Superfamily superfamily	d.212.1 — TolA/TonB C-terminal domain
家族 Family family	d.212.1.2 — TonB

CATH v4.4 (6 domains)

结构域编号 domain_id	2grxA01
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	2grxA02
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

结构域编号 domain_id	2grxB01
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	2grxB02
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

结构域编号 domain_id	2grxC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2420 — TolA/TonB C-terminal domain
同源超家族 H-superfamily homologous superfamily	10 — TonB

结构域编号 domain_id	2grxD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2420 — TolA/TonB C-terminal domain
同源超家族 H-superfamily homologous superfamily	10 — TonB

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7. 引用文献 (1)

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晶胞边长 a length_a	234.320 Å
晶胞边长 b length_b	91.840 Å
晶胞边长 c length_c	138.510 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	118.86 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.300 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2990
R_work r_work	0.2840
R_free r_free	0.3290

fit	/app/data/saxs_computation/gr/2grx/2grx.fit
pddf	/app/data/pr_computation/gr/2grx/2grx.pr.out
profile	/app/data/saxs_computation/gr/2grx/2grx.dat

Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for ferrichrome

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 (10)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)