2dhh

Crystal structure of a multidrug transporter reveal a functionally rotating mechanism

Method: X-RAY DIFFRACTION Dmax: 140.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 2dhh

P(r) 距离分布 P(r) Distribution

P(r) distribution for 2dhh
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id2dhh
沉积日期 deposition_date2006-03-23
结构标题 titleCrystal structure of a multidrug transporter reveal a functionally rotating mechanism
关键词 keywordsmembrane transporter, membrane protein, multidrug efflux, drug resistance, transporter, exporter, antiporter; MEMBRANE PROTEIN
实验方法 methodX-RAY DIFFRACTION

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier45.49
回转半径 Rg (电子) rg_electron44.92
零角强度 I(0) i01451600000.00
分子量 molecular_weight331710.0 kDa
排除体积 excluded_volume421500 ų
包络体积 envelope_volume558320 ų
水化壳体积 shell_volume98214 ų
包络直径 envelope_diameter144.5
壳层 Rg shell_rg53.82
包络 Rg envelope_rg44.11
形状 Rg shape_rg44.92
总 Rg total_rg45.24
总原子数 total_atoms23322
残基数 n_residues3066
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax140.5
Rg (实空间) rg_real45.22
Rg 误差 (实空间) rg_real_error0.78
I(0) (实空间) i0_real1.4520e+09
I(0) 误差 (实空间) i0_real_error2.5110e+07
Rg (倒空间) rg_reciprocal45.49
I(0) (倒空间) i0_reciprocal1452000000.0000
解质量估计 total_estimate0.8782
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary60.2
偏度 Skewness skewness0.145
峰度 Kurtosis kurtosis-0.432
角度范围 angular_range— – 0.1750 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha234700000.0000
实空间数据点数 n_real_points36
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.699

4. 晶体学与实验 4. Crystallography & Experiment

5. 实体与聚合体信息 (2)

6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

结构域编号 domain_idd2dhha1
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.35 — Multidrug efflux transporter AcrB transmembrane domain
超家族 Superfamily superfamilyf.35.1 — Multidrug efflux transporter AcrB transmembrane domain
家族 Family familyf.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_idd2dhha2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhha3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhha4
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
超家族 Superfamily superfamilyd.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
家族 Family familyd.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_idd2dhha5
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.35 — Multidrug efflux transporter AcrB transmembrane domain
超家族 Superfamily superfamilyf.35.1 — Multidrug efflux transporter AcrB transmembrane domain
家族 Family familyf.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_idd2dhha6
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhha7
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhha8
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
超家族 Superfamily superfamilyd.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
家族 Family familyd.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_idd2dhhb1
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.35 — Multidrug efflux transporter AcrB transmembrane domain
超家族 Superfamily superfamilyf.35.1 — Multidrug efflux transporter AcrB transmembrane domain
家族 Family familyf.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_idd2dhhb2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhhb3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhhb4
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
超家族 Superfamily superfamilyd.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
家族 Family familyd.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_idd2dhhb5
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.35 — Multidrug efflux transporter AcrB transmembrane domain
超家族 Superfamily superfamilyf.35.1 — Multidrug efflux transporter AcrB transmembrane domain
家族 Family familyf.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_idd2dhhb6
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhhb7
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhhb8
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
超家族 Superfamily superfamilyd.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
家族 Family familyd.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_idd2dhhc1
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.35 — Multidrug efflux transporter AcrB transmembrane domain
超家族 Superfamily superfamilyf.35.1 — Multidrug efflux transporter AcrB transmembrane domain
家族 Family familyf.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_idd2dhhc2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhhc3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhhc4
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
超家族 Superfamily superfamilyd.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
家族 Family familyd.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_idd2dhhc5
类 Class classf — Membrane and cell surface proteins and peptides
折叠类型 Fold foldf.35 — Multidrug efflux transporter AcrB transmembrane domain
超家族 Superfamily superfamilyf.35.1 — Multidrug efflux transporter AcrB transmembrane domain
家族 Family familyf.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_idd2dhhc6
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhhc7
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
家族 Family familyd.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
结构域编号 domain_idd2dhhc8
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
超家族 Superfamily superfamilyd.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
家族 Family familyd.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

CATH v4.4 (24 domains)

结构域编号 domain_id2dhhA01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1640 — Multidrug efflux transporter AcrB transmembrane fold
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_id2dhhA02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1430 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhA03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1320 — Multidrug efflux transporter AcrB pore domain like
结构域编号 domain_id2dhhA04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_id2dhhA05
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1640 — Multidrug efflux transporter AcrB transmembrane fold
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_id2dhhA06
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1430 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhA07
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1440 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhA08
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_id2dhhB01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1640 — Multidrug efflux transporter AcrB transmembrane fold
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_id2dhhB02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1430 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhB03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1320 — Multidrug efflux transporter AcrB pore domain like
结构域编号 domain_id2dhhB04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_id2dhhB05
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1640 — Multidrug efflux transporter AcrB transmembrane fold
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_id2dhhB06
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1430 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhB07
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1440 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhB08
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_id2dhhC01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1640 — Multidrug efflux transporter AcrB transmembrane fold
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_id2dhhC02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1430 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhC03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1320 — Multidrug efflux transporter AcrB pore domain like
结构域编号 domain_id2dhhC04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
结构域编号 domain_id2dhhC05
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1640 — Multidrug efflux transporter AcrB transmembrane fold
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB transmembrane domain
结构域编号 domain_id2dhhC06
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1430 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhC07
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1440 — Multidrug efflux transporter AcrB pore domain
结构域编号 domain_id2dhhC08
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
同源超家族 H-superfamily homologous superfamily10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

7. 引用文献 (1)

8. 文件与曲线 (10)