1oy9

Structural Basis of Multiple Drug Binding Capacity of the AcrB Multidrug Efflux Pump

Method: X-RAY DIFFRACTION D_max: 125.1 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	1oy9
沉积日期 deposition_date	2003-04-03
结构标题 title	Structural Basis of Multiple Drug Binding Capacity of the AcrB Multidrug Efflux Pump
关键词 keywords	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	36.80 Å
回转半径 Rg (电子) rg_electron	36.92 Å
零角强度 I(0) i0	167222000.00
分子量 molecular_weight	108950.0 kDa
排除体积 excluded_volume	138550 Å³
包络体积 envelope_volume	183540 Å³
水化壳体积 shell_volume	43951 Å³
包络直径 envelope_diameter	133.2 Å
壳层 Rg shell_rg	40.04 Å
包络 Rg envelope_rg	37.01 Å
形状 Rg shape_rg	36.91 Å
总 Rg total_rg	37.17 Å
总原子数 total_atoms	7663
残基数 n_residues	1006
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	125.1 Å
Rg (实空间) rg_real	37.17 Å
Rg 误差 (实空间) rg_real_error	1.17 Å
I(0) (实空间) i0_real	1.6720e+08
I(0) 误差 (实空间) i0_real_error	3.1020e+06
Rg (倒空间) rg_reciprocal	36.94 Å
I(0) (倒空间) i0_reciprocal	167200000.0000
解质量估计 total_estimate	0.8112
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	34.9 Å
偏度 Skewness skewness	0.605
峰度 Kurtosis kurtosis	-0.121
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26950000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.823; Smooth: 0.486

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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)

Entity 1 polymer

描述 description	Acriflavine resistance protein B
分子量 formula_weight	113665.2 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	7663

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHH

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 non-polymer

描述 description	ETHIDIUM
分子量 formula_weight	314.4 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) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1oy9a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family family	d.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains

结构域编号 domain_id	d1oy9a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family family	d.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains

结构域编号 domain_id	d1oy9a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family family	d.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains

结构域编号 domain_id	d1oy9a4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family family	d.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains

结构域编号 domain_id	d1oy9a5
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
超家族 Superfamily superfamily	d.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
家族 Family family	d.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

结构域编号 domain_id	d1oy9a6
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
超家族 Superfamily superfamily	d.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
家族 Family family	d.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

结构域编号 domain_id	d1oy9a7
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.35 — Multidrug efflux transporter AcrB transmembrane domain
超家族 Superfamily superfamily	f.35.1 — Multidrug efflux transporter AcrB transmembrane domain
家族 Family family	f.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain

结构域编号 domain_id	d1oy9a8
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.35 — Multidrug efflux transporter AcrB transmembrane domain
超家族 Superfamily superfamily	f.35.1 — Multidrug efflux transporter AcrB transmembrane domain
家族 Family family	f.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1oy9A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
同源超家族 H-superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

结构域编号 domain_id	1oy9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

结构域编号 domain_id	1oy9A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1320 — Multidrug efflux transporter AcrB pore domain like

结构域编号 domain_id	1oy9A04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
同源超家族 H-superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

结构域编号 domain_id	1oy9A05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
同源超家族 H-superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

结构域编号 domain_id	1oy9A06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

结构域编号 domain_id	1oy9A07
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1440 — Multidrug efflux transporter AcrB pore domain

结构域编号 domain_id	1oy9A08
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
同源超家族 H-superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

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7. 引用文献 (1)

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晶胞边长 a length_a	144.676 Å
晶胞边长 b length_b	144.676 Å
晶胞边长 c length_c	517.512 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	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	3.800 Å
最低分辨率 resolution_low	46.600 Å
R 因子 r_factor	0.2860
R_work r_work	0.2830
R_free r_free	0.3440

fit	/app/data/saxs_computation/oy/1oy9/1oy9.fit
pddf	/app/data/pr_computation/oy/1oy9/1oy9.pr.out
profile	/app/data/saxs_computation/oy/1oy9/1oy9.dat

Structural Basis of Multiple Drug Binding Capacity of the AcrB Multidrug Efflux Pump

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