29on

Crystal structure of the staphylococcal efflux pump QacA in the inward open state in complex with nanobody 89

Method: X-RAY DIFFRACTION D_max: 121.0 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	29on
沉积日期 deposition_date	2026-03-26
最后修订 last_revision	2026-04-22
结构标题 title	Crystal structure of the staphylococcal efflux pump QacA in the inward open state in complex with nanobody 89
关键词 keywords	;Multidrug efflux pump, Major Facilitator Superfamily, MFS, DHA2 family, Antimicrobial resistance, Drug resistance, Proton-coupled transport, Drug-proton antiport, Membrane protein, 14-transmembrane helix, Secondary active transporter, Cationic substrate efflux, Nanobody, Single-domain Indian camelid antibody ;; 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	38.71 Å
回转半径 Rg (电子) rg_electron	38.09 Å
零角强度 I(0) i0	221808000.00
分子量 molecular_weight	132580.0 kDa
排除体积 excluded_volume	170790 Å³
包络体积 envelope_volume	224590 Å³
水化壳体积 shell_volume	48435 Å³
包络直径 envelope_diameter	125.2 Å
壳层 Rg shell_rg	45.16 Å
包络 Rg envelope_rg	36.82 Å
形状 Rg shape_rg	38.08 Å
总 Rg total_rg	38.60 Å
总原子数 total_atoms	9333
残基数 n_residues	1233
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	121.0 Å
Rg (实空间) rg_real	38.56 Å
Rg 误差 (实空间) rg_real_error	1.02 Å
I(0) (实空间) i0_real	2.2180e+08
I(0) 误差 (实空间) i0_real_error	3.5170e+06
Rg (倒空间) rg_reciprocal	38.66 Å
I(0) (倒空间) i0_reciprocal	221800000.0000
解质量估计 total_estimate	0.8982
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	62.0 Å
偏度 Skewness skewness	0.063
峰度 Kurtosis kurtosis	-0.804
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31530000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.928

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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 (6)

Entity 1 polymer

描述 description	Antiseptic resistance protein
分子量 formula_weight	55784.3 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	9333

MISFFTKTTDMMTSKKRWTALVVLAVSLFVVTMDMTILIMALPELVRELEPSGTQQLWIVDIYSLVLAGFIIPLSAFADKWGRKKALLTGFALFGLVSLAIFFAESAEFVIAIRFLLGIAGALIMPTTLSMIRVIFENPKERATALAVWSIASSIGAVFGPIIGGALLEQFSWHSAFLINVPFAIIAVVAGLFLLPESKLSKEKSHSWDIPSTILSIAGMIGLVWSIKEFSKEGLADIIPWVVIVLAITMIVIFVKRNLSSSDPMLDVRLFKKRSFSAGTIAAFMTMFAMASVLLLASQWLQVVEELSPFKAGLYLLPMAIGDMVFAPIAPGLAARFGPKIVLPSGIGIAAIGMFIMYFFGHPLSYSTMALALILVGAGMASLAVASALIMLETPTSKAGNAAAVEESMYDLGNVFGVAVLGSLSSMLYRVFLDISSFSSKGIVGDLAHVAEESVVGAVEVAKATGIKQLANEAVTSFNDAFVATALVGGIIMIIISIVVYLLIPKSLDITKQKLEVLFQ

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI 分类编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Nanobody 89
分子量 formula_weight	15965.6 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

MAQVQLVESGGGLVQAGGSLKLSCAASGRTFSSAYMGWFRQAPGKEREFVAAIKWSGGSTYYAHSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATKGNPNSYEYDVWGQGTQVTVSSAAAHHHHHHGAAEQKLISEEDLNGAA

来源 Source

来源生物 organism	Lama glama
NCBI 分类编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	PHOSPHATIDYLETHANOLAMINE
分子量 formula_weight	734.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
分子量 formula_weight	751.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	DODECYL-ALPHA-D-MALTOSIDE
分子量 formula_weight	510.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	OXAMIC ACID
分子量 formula_weight	89.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	188.304 Å
晶胞边长 b length_b	94.335 Å
晶胞边长 c length_c	98.306 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.47 °
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	3.320 Å
最低分辨率 resolution_low	31.530 Å
R 因子 r_factor	0.2986
R_work r_work	0.2972
R_free r_free	0.3265

fit	/app/data/saxs_computation/9o/29on/29on.fit
pddf	/app/data/pr_computation/9o/29on/29on.pr.out
profile	/app/data/saxs_computation/9o/29on/29on.dat

Crystal structure of the staphylococcal efflux pump QacA in the inward open state in complex with nanobody 89

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)