8hpj

Crystal structure of the bacterial oxalate transporter OxlT in a ligand-free outward-facing form

Method: X-RAY DIFFRACTION D_max: 158.3 Å Quality: REASONABLE

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	8hpj
沉积日期 deposition_date	2022-12-12
结构标题 title	Crystal structure of the bacterial oxalate transporter OxlT in a ligand-free outward-facing form
关键词 keywords	Transporter, TRANSPORT PROTEIN, TRANSPORT PROTEIN-IMMUNE SYSTEM complex; TRANSPORT PROTEIN/IMMUNE SYSTEM
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	42.05 Å
回转半径 Rg (电子) rg_electron	43.22 Å
零角强度 I(0) i0	241899000.00
分子量 molecular_weight	134760.0 kDa
排除体积 excluded_volume	171870 Å³
包络体积 envelope_volume	225250 Å³
水化壳体积 shell_volume	48253 Å³
包络直径 envelope_diameter	158.3 Å
壳层 Rg shell_rg	42.56 Å
包络 Rg envelope_rg	42.67 Å
形状 Rg shape_rg	43.21 Å
总 Rg total_rg	43.20 Å
总原子数 total_atoms	9517
残基数 n_residues	1253
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	158.3 Å
Rg (实空间) rg_real	42.53 Å
Rg 误差 (实空间) rg_real_error	2.39 Å
I(0) (实空间) i0_real	2.4190e+08
I(0) 误差 (实空间) i0_real_error	5.5160e+06
Rg (倒空间) rg_reciprocal	42.05 Å
I(0) (倒空间) i0_reciprocal	241800000.0000
解质量估计 total_estimate	0.7331
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	41.7 Å
偏度 Skewness skewness	0.654
峰度 Kurtosis kurtosis	0.028
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18910000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.600; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.726; Smooth: 0.000

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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 (3)

Entity 1 polymer

描述 description	Oxalate:formate antiporter
分子量 formula_weight	45787.3 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,D
原子数 atom_count	9517

MNNPQTGQSTGLLGNRWFYLVLAVLLMCMISGVQYSWTLYANPVKDNLGVSLAAVQTAFTLSQVIQAGSQPGGGYFVDKFGPRIPLMFGGAMVLAGWTFMGMVDSVPALYALYTLAGAGVGIVYGIAMNTANRWFPDKRGLASGFTAAGYGLGVLPFLPLISSVLKVEGVGAAFMYTGLIMGILIILIAFVIRFPGQQGAKKQIVVTDKDFNSGEMLRTPQFWVLWTAFFSVNFGGLLLVANSVPYGRSLGLAAGVLTIGVSIQNLFNGGCRPFWGFVSDKIGRYKTMSVVFGINAVVLALFPTIAALGDVAFIAMLAIAFFTWGGSYALFPSTNSDIFGTAYSARNYGFFWAAKATASIFGGGLGAAIATNFGWNTAFLITAITSFIAFALATFVIPRMGRPVKKMVKLSPEEKAVHHHHHHHHHH

来源 Source

来源生物 organism	Oxalobacter formigenes
NCBI 分类编号 ncbi_taxonomy_id	847
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Fv fragment Heavy chain
分子量 formula_weight	15111.0 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	B,E

LEVMLVESGGGLVKPGGSLKLSCAASGFTFSNYAMSWVRQTPEKRLEWVALISSGGYTYYPDSVKGRFTISRDKARNILHLQMSSLRSEDTAMYFCARGPYDFDDGPPFGNWGQGTLVTVSAAKTTAPSVTSENLYFQ

来源 Source

来源生物 organism	Mus musculus
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Brevibacillus choshinensis

Entity 3 polymer

描述 description	Fv fragment Light chain
分子量 formula_weight	12947.3 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	C,F

ELDIVLTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQYNSYPLTFGAGTKLELKTSENLYFQ

来源 Source

来源生物 organism	Mus musculus
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Brevibacillus choshinensis

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6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	8hpjB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8hpjC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8hpjE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8hpjF01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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晶胞边长 a length_a	76.870 Å
晶胞边长 b length_b	181.670 Å
晶胞边长 c length_c	81.170 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.36 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	3.300 Å
最低分辨率 resolution_low	47.260 Å
R 因子 r_factor	0.2610
R_work r_work	0.2596
R_free r_free	0.2859

fit	/app/data/saxs_computation/hp/8hpj/8hpj.fit
pddf	/app/data/pr_computation/hp/8hpj/8hpj.pr.out
profile	/app/data/saxs_computation/hp/8hpj/8hpj.dat

Crystal structure of the bacterial oxalate transporter OxlT in a ligand-free outward-facing form

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)