SAXSdb — 8pc0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8pc0
沉积日期 deposition_date	2023-06-09
结构标题 title	Sub-tomogram average of the open conformation of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.
关键词 keywords	Adhesion, Mycoplasma genitalium, CELL ADHESION; CELL ADHESION
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	40.98 Å
回转半径 Rg (电子) rg_electron	40.01 Å
零角强度 I(0) i0	858825000.00
分子量 molecular_weight	239420.0 kDa
排除体积 excluded_volume	298590 Å³
包络体积 envelope_volume	394700 Å³
水化壳体积 shell_volume	78155 Å³
包络直径 envelope_diameter	131.4 Å
壳层 Rg shell_rg	48.67 Å
包络 Rg envelope_rg	39.84 Å
形状 Rg shape_rg	39.97 Å
总 Rg total_rg	40.56 Å
总原子数 total_atoms	33314
残基数 n_residues	2172
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	128.1 Å
Rg (实空间) rg_real	40.82 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	8.5880e+08
I(0) 误差 (实空间) i0_real_error	1.3760e+07
Rg (倒空间) rg_reciprocal	40.98 Å
I(0) (倒空间) i0_reciprocal	859000000.0000
解质量估计 total_estimate	0.8993
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.2 Å
偏度 Skewness skewness	0.181
峰度 Kurtosis kurtosis	-0.553
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	229500000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.889

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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	Mgp-operon protein 3
分子量 formula_weight	114553.2 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	33611

MKTMRKQIYKKAYWLLLPFLPLALANTFLVKEDSKNVTAYTPFATPITDSKSDLVSLAQLDSSYQIADQTIHNTNLFVLFKSRDVKVKYESSGSNNISFDSTSQGEKPSYVVEFTNSTNIGIKWTMVKKYQLDVPNVSSDMNQVLKNLILEQPLTKYTLNSSLAKEKGKTQREVHLGSGQANQWTSQRNQHDLNNNPSPNASTGFKLTTGNAYRKLSESWPIYEPIDGTKQGKGKDSSGWSSTEENEAKNDAPSVSGGGSSSGTFNKYLNTKQALESIGILFDDQTPRNVITQLYYASTSKLAVTNNHIVVMGNSFLPSMWYWVVERSAQENASNKPTWFANTNLDWGEDKQKQFVENQLGYKETTSTNSHNFHSKSFTQPAYLISGIDSVNDQIIFSGFKAGSVGYDSSSSSSSSSSSSTKDQALAWSTTTSLDSKTGYKDLVTNDTGLNGPINGSFSIQDTFSFVVPYSGNHTNNGTTGPIKTAYPVKKDQKSTVKINSLINATPLNSYGDEGIGVFDALGLNYNFKSNQERLPSRTDQIFVYGIVSPNELRSAKSSADSTGSDTKVNWSNTQSRYLPVPYNYSEGIIDADGFKRPENRGASVTTFSGLKSIAPDGFANSIANFSVGLKAGIDPNPVMSGKKANYGAVVLTRGGVVRLNFNPGNDSLLSTTDNNIAPISFSFTPFTAAESAVDLTTFKEVTYNQESGLWSYIFDSSLKPSHDGKQTPVTDNMGFSVITVSRTGIELNQDQATTTLDVAPSALAVQSGIQSTTQTLTGVLPLSEEFSAVIAKDSDQNKIDIYKNNNGLFEIDTQLSNSVATNNGGLAPSYTENRVDAWGKVEFADNSVLQARNLVDKTVDEIINTPEILNSFFRFTPAFEDQKATLVATKQSDTSLSVSPRIQFLDGNFYDLNSTIAGVPLNIGFPSRVFAGFAALPAWVIPVSVGSSVGILFILLVLGLGIGIPMYRVRKLQDASFVNVFKKVDTLTTAVGSVYKKIITQTGVVKKAPSALKAANPSVKKPAAFLKPPVQPPSKPEGEQKAVEVKSEETKS

Entity 2 polymer

描述 description	Adhesin P1
分子量 formula_weight	159809.3 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	C

MHQPKKRLAKKSWAFLTAALTLGVITGVGGYFLFNQNKQRSSVSNFAYQPKQLSVKHQQAVDETLTPWTWNNNNFSSLKITGENPGSFGLVRSQNDNLNISSVTKNSSDDNLKYLNAVEKYLDGQQNFAIRRYDNNGRALYDINLAKMENPSTVQRGLNGEPIFDPFKGFGLTGNAPTDWNEIKGKVPVEVVQSPHSPNLYFVLLVPKVALEYHNLNNQVVKESLEVKATQSSFNPTQRLQKDSPVKDSSKQGEKLSETTASSMSSGMATSTRAKALKVEVERGSQSDSLLKNDFAKKPLKHKNSSGEVKLEAEKEFTEAWKPLLTTDQIAREKGMGATVVSFYDAPYSENHTAFGLVDHIDPKKMVENYPPSWKTPKWNHHGIWDYNARNLLLQTTGFFNPRRHPEWFDEGQAKADNTSPGFKVGDTDHKKDGFKKNSSSPIALPFEAYFANIGNMVAIGNSVFIFGGNGHATKMFTTNPLSIGVFRIKYTDNFSKSSVTGWPYAVLFGGLINPQTNGLKDLPLGTNRWFEYVPRMAVSGVKWVGNQLVLAGTLTMGDTATVPRLKYDQLEKHLNLVAQGQGLLREDLQIFTPYGWANRPDIPVGAWLQDEMGSKFGPHYFLNNPDIQDNVNNDTVEALISSYKNTDKLKHVYPYRYSGLYAWQLFNWSNKLTNTPLSANFVNENSYAPNSLFAAILNEDLLTGLSDKIFYGKENEFAENEADRFNQLLSLNPNPNTNWARYLNVVQRFTTGPNLDSSTFDQFLDFLPWIGNGKPFSNSPSPSTSASSSTPLPTFSNINVGVKSMITQHLNKENTRWVFIPNFSPDIWTGAGYRVQSANQKNGIPFEQVKPSNNSTPFDPNSDDNKVTPSGGSSKPTTYPALPNSISPTSDWINALTFTNKNNPQRNQLLLRSLLGTIPVLINKSGDSNDQFNKDSEQKWDKTETNEGNLPGFGEVNGLYNAALLHTYGFFGTNTNSTDPKIGFKADSSSSSSSTLVGSGLNWTSQDVGNLVVINDTSFGFQLGGWFITFTDFIRPRTGYLGITLSSLQDQTIIWADQPWTSFKGSYLDSDGTPKSLWDPTALKSLPNSSTTYDTNPTLSPSFQLYQPNKVKAYQTTNTYNKLIEPVDATSAATNMTSLLKLLTTKNIKAKLGKGTASSQGNNNGGGVSQTINTITTTGNISEGLKEETSIQAETLKKFFDSKQNNKSEIGIGDSTFTKMDGKLTGVVSTPLVNLINGQGATSDSDTEKISFKPGNQIDFNRLFTLPVTELFDPNTMFVYDQYVPLLVNLPSGFDQASIRLKVISYSVENQTLGVRLEFKDPQTQQFIPVLNASSTGPQTVFQPFNQWADYVLPLIVTVPIVVIILSVTLGLTIGIPMHRNKKALQAGFDLSNKKVDVLTKAVGSVFKEIINRTGISNAPKKLKQATPTKPTPKTPPKPPVKQ

Entity 3 branched

描述 description	N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-1,5-anhydro-D-glucitol
分子量 formula_weight	617.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	99

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7. 引用文献 (1)

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分辨率 resolution	17.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	9689

fit	/app/data/saxs_computation/pc/8pc0/8pc0.fit
pddf	/app/data/pr_computation/pc/8pc0/8pc0.pr.out
profile	/app/data/saxs_computation/pc/8pc0/8pc0.dat

Sub-tomogram average of the open conformation of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.

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

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 non-polymer

Entity 5 non-polymer

Entity 6 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)