SAXSdb — 1qjq

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qjq
沉积日期 deposition_date	1999-06-29
结构标题 title	FERRIC HYDROXAMATE RECEPTOR FROM ESCHERICHIA COLI (FHUA)
关键词 keywords	;TONB DEPENDENT RECEPTOR, LIPOPOLYSACCHARIDE, FERRICHROME-IRON RECEPTOR, INTEGRAL OUTER MEMBRANE PROTEIN, TONB-DEPENDENT RECEPTOR, SIDEROPHORE RECEPTOR, ACTIVE TRANSPORT, IRON TRANSPORT, SIDEROPHORE-ANTIBIOTIC CONJUGATE ;; TONB DEPENDENT RECEPTOR
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	26.54 Å
回转半径 Rg (电子) rg_electron	25.71 Å
零角强度 I(0) i0	115158000.00
分子量 molecular_weight	82674.0 kDa
排除体积 excluded_volume	102370 Å³
包络体积 envelope_volume	120910 Å³
水化壳体积 shell_volume	37696 Å³
包络直径 envelope_diameter	87.3 Å
壳层 Rg shell_rg	34.62 Å
包络 Rg envelope_rg	25.91 Å
形状 Rg shape_rg	25.71 Å
总 Rg total_rg	26.53 Å
总原子数 total_atoms	5823
残基数 n_residues	707
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	83.2 Å
Rg (实空间) rg_real	26.39 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	1.1520e+08
I(0) 误差 (实空间) i0_real_error	1.6470e+06
Rg (倒空间) rg_reciprocal	26.44 Å
I(0) (倒空间) i0_reciprocal	115200000.0000
解质量估计 total_estimate	0.8935
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	34.7 Å
偏度 Skewness skewness	0.215
峰度 Kurtosis kurtosis	-0.316
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19690000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.977

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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 (8)

Entity 1 polymer

描述 description	FERRIC HYDROXAMATE RECEPTOR
分子量 formula_weight	80051.1 kDa
突变 mutation	YES
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	6218

AVEPKEDTITVTAAPAPQESAWGPAATIAARQSATGTKTDTPIQKVPQSISVVTAEEMALHQPKSVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAVIDPYMLERAEIMRGPVSVLYGKSSPGGLLNMVSKRPTTEPLKEVQFKAGTDSLFQTGFDFSDSLDDDGVYSYRLTGLARSANAQQKGSEEQRYAIAPAFTWRPDDKTNFTFLSYFQNEPETGYYGWLPKEGTVEPLPNGKRLPTDFNEGAKNNTYSRNEKMVGYSFDHEFNDTFTVRQNLRFAENKTSQNSVYGYGVCSDPANAYSKQCAALAPADKGHYLARKYVVDDEKLQNFSVDTQLQSKFATGDIDHTLLTGVDFMRMRNDINAWFGYDDSVPLLNLYNPSSHHHHHHGSSVNTDFDFNAKDPANSGPYRILNKQKQTGVYVQDQAQWDKVLVTLGGRYDWADQESLNRVAGTTDKRDDKQFTWRGGVNYLFDNGVTPYFSYSESFEPSSQVGKDGNIFAPSKGKQYEVGVKYVPEDRPIVVTGAVYNLTKTNNLMADPEGSFFSVEGGEIRARGVEIEAKAALSASVNVVGSYTYTDAEYTTDTTYKGNTPAQVPKHMASLWADYTFFDGPLSGLTLGTGGRYTGSSYGDPANSFKVGSYTVVDALVRYDLARVGMAGSNVALHVNNLFDREYVASCFNTYGCFWGAERQVVATATFRF

来源 Source

来源生物 organism	ESCHERICHIA COLI
通用名 common_name	E. COLI
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	ESCHERICHIA COLI K-12

Entity 2 branched

描述 description	;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]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	1973.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 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	6

Entity 4 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 5 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 6 non-polymer

描述 description	NICKEL (II) ION
分子量 formula_weight	58.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	PHENYLFERRICROCIN-IRON
分子量 formula_weight	830.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	395

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1qjqa_
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

CATH v4.4 (2 domains)

结构域编号 domain_id	1qjqA01
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	1qjqA02
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 (3)

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晶胞边长 a length_a	172.100 Å
晶胞边长 b length_b	172.100 Å
晶胞边长 c length_c	87.650 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	2.950 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2780

fit	/app/data/saxs_computation/qj/1qjq/1qjq.fit
pddf	/app/data/pr_computation/qj/1qjq/1qjq.pr.out
profile	/app/data/saxs_computation/qj/1qjq/1qjq.dat

FERRIC HYDROXAMATE RECEPTOR FROM ESCHERICHIA COLI (FHUA)

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution