9p6h

Structure of P. gingivalis PorK and PorN complexes from cryo electron microscopy

Method: ELECTRON MICROSCOPY D_max: 101.1 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	9p6h
沉积日期 deposition_date	2025-06-19
结构标题 title	Structure of P. gingivalis PorK and PorN complexes from cryo electron microscopy
关键词 keywords	T9SS, porphyromonas gingivalis, TRANSPORT PROTEIN; TRANSPORT PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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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	30.88 Å
回转半径 Rg (电子) rg_electron	30.17 Å
零角强度 I(0) i0	117023000.00
分子量 molecular_weight	84554.0 kDa
排除体积 excluded_volume	105300 Å³
包络体积 envelope_volume	141000 Å³
水化壳体积 shell_volume	39057 Å³
包络直径 envelope_diameter	108.6 Å
壳层 Rg shell_rg	37.10 Å
包络 Rg envelope_rg	30.27 Å
形状 Rg shape_rg	30.16 Å
总 Rg total_rg	30.86 Å
总原子数 total_atoms	5963
残基数 n_residues	701
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	101.1 Å
Rg (实空间) rg_real	30.86 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	1.1700e+08
I(0) 误差 (实空间) i0_real_error	1.6940e+06
Rg (倒空间) rg_reciprocal	30.87 Å
I(0) (倒空间) i0_reciprocal	117000000.0000
解质量估计 total_estimate	0.8930
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	35.7 Å
偏度 Skewness skewness	0.343
峰度 Kurtosis kurtosis	-0.325
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19670000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.962

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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	Gliding motility protein GldN
分子量 formula_weight	30080.9 kDa
来源方法 src_method	nat
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	5963

LSNRAQEFNRRLTQKTDNAPWRRVVYRRVDLMEESNAVLYYPPRPIGDRKNLFSTIFGLINSNSLDVYEYLDGFEAFTDQYKIKFQEFLDRFGIYYQPSTNKNAELFKVADSDIPSAEVKAYYVKEEWYFTPTNSDVDIKIQAICPIMTGQDEFGEVRNQPLFWIPYENIRPYIARERVMLSSLNNTRNSTIDDFFRLNLYKGDIVKTENLHNRALAEYCPTPDSMKMESKRIDKELQGFRDGLFVTQDTTWMK

Entity 2 polymer

描述 description	Lipoprotein, putative
分子量 formula_weight	51184.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

ELTGAKLSSWNEPSPFGMIQVPRGSIVLGNKEADSLWGIPAESRPISVDAFWMDRTEITNAQYRQFVYYVRDSIIRERLADPAYGGNEEYKITENKFGEPVTPHLDWSKPIPSEKRATEEEIAAINSVYYTNPVTHDRKLNPDQMVYRYEVYDYRSAALREHQLKAAKRNLNTDIKVDPNAVVMISKDTAFVDESGNIISETITRPLSSEYDFLNTYIVPIYPDETCWVNDFPNARTEIYTRMYFNHPGYDDYPVVGISWEQAQAFCAWRSEFFRKGIRLPEGQIMDDFRLPTEAEWEYAARMGDSNNKYPWSTEDLRTGRGCFLGNFKPGEGDYTADGHLIPSRVSSFSPNDFGLYDMAGNVAEWTSTAFSESGLKQMSDINPELEYKAALTDPYILKQKVVRGGSWKDVARFIRSATRSHEYQNVGRSYIGFRCVRTSIAFSSGK

Entity 3 branched

描述 description	;2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-L-fucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose ;
分子量 formula_weight	1217.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

Entity 4 branched

描述 description	beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose
分子量 formula_weight	664.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	beta-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (2)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.750 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	2.75 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	69982

fit	/app/data/saxs_computation/p6/9p6h/9p6h.fit
pddf	/app/data/pr_computation/p6/9p6h/9p6h.pr.out
profile	/app/data/saxs_computation/p6/9p6h/9p6h.dat

Structure of P. gingivalis PorK and PorN complexes from cryo electron microscopy

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)