SAXSdb — 9kz7

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9kz7
沉积日期 deposition_date	2024-12-10
结构标题 title	The cryo-EM structure of porcine serum MGAM bound with Acarviosyl-maltotriose.
关键词 keywords	alpha-glucosidase, HYDROLASE; HYDROLASE
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	45.21 Å
回转半径 Rg (电子) rg_electron	44.86 Å
零角强度 I(0) i0	621416000.00
分子量 molecular_weight	207260.0 kDa
排除体积 excluded_volume	259030 Å³
包络体积 envelope_volume	330460 Å³
水化壳体积 shell_volume	61243 Å³
包络直径 envelope_diameter	155.6 Å
壳层 Rg shell_rg	49.42 Å
包络 Rg envelope_rg	44.24 Å
形状 Rg shape_rg	44.84 Å
总 Rg total_rg	45.12 Å
总原子数 total_atoms	14642
残基数 n_residues	1771
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	152.2 Å
Rg (实空间) rg_real	45.37 Å
Rg 误差 (实空间) rg_real_error	1.42 Å
I(0) (实空间) i0_real	6.2140e+08
I(0) 误差 (实空间) i0_real_error	1.1880e+07
Rg (倒空间) rg_reciprocal	45.22 Å
I(0) (倒空间) i0_reciprocal	621300000.0000
解质量估计 total_estimate	0.8574
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	39.1 Å
偏度 Skewness skewness	0.329
峰度 Kurtosis kurtosis	-0.674
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	147300000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.855; Smooth: 0.842

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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 (5)

Entity 1 polymer

描述 description	Maltase-glucoamylase
分子量 formula_weight	203509.7 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	14659

VLSARESLESKDAGTPGPSTPDSAECAVANELERINCIPDQSPTKATCDQRGCCWKPQGAISVPWCYYSTNHGYQVEGDLVNTNAGFTAQLKRLPSPSLFGNDINNVLLRAEYQTATRFHFKLTDQNQDRYEVPHEHVQPFQGNAASPLTYEVMVSKQPFSIKVIRTSNSRVLFDSSIGPLLFADQFLQLSIRLPSANVYGLGEHVHQQYRHDMNWKTWPIFARDTVPNGDGNNLYGAQTFFLCLEDASGLSFGVFLMNSNAMEVALQPAPAVTYRTTGGILDFYVLLGNTPEQVVQEYLQLIGLPALPPYWALGFHLSRYDYETLDNMREVVERNRAAQLPYDVQHADIDYMDKRRDFTYNPVDFKGFPELAQDLHNNGQKLVIIVDPAISNDSSPSSPYGPYDRGSDAKIWVNDPDGVTPLIGEVWPGKTVFPDYTNPKCTTWWENEFKLFHNQVDFDGIWIDMNEVANFVDGSVSGCSTSNLNYPPFTPRILDGYLFSKTLCMDAVQHWGKQYDVHNLYGYSMAIATAEAVKTVFSNKRSFILTRSTFAGSGKFAAHWLGDNAATWDDLRWSIPGMLEFNLFGIPMVGSDICGFLLDTSEELCRRWMQVGAFYPFSRNHNGQGYKVQDPASFGADSLLLNSSRHYLSIRYTLLPYLYTLFYHAHSRGDTVARPLLHEFYEDSNTWDVYQQFLWGPGLLITPVLDEGAEKVTAYVPDAVWYDYETGGRVTWRKQKVEMELPGDKIGLHLRGGYIFPTQQPATTTVASRQNPLGLIIALDDNKEAKGELFWDDGEAKDTVANKVYLLYEFSVTQNRLDVKILQSTYTDPNNLVFKEIKILGTQEPSNVIVKQNDIPVQVSPNVAYDSNLQVALITEIELELGKNYTVEWDVKIRDEEKIDCYPDETGASEGNCVARGCAWEASTSPGVPHCYFVDELYSVSDVQYDSFGATAAISLKSSLYASALPSVPVNSLRLSVTYHKENMLQFKIYDPSNNRYEVPVPLNVPRVPSGTSESRLYDVLIKKNPFGIEIRRKSTGTVIWDSQLLGFTFNDMFIQISTRLPSQYLYGFGETEHTAFRRNLNWHTWGMFSRDQPPGYKMNSYGVHPYYMALEEDGNAHGVLLLNSNAMDVTFQPLPALTYRTTGGILDFYVLLGPTPELVTQQYTELIGRPVMVPYWSLGFQLCRYGYENDSEIASLYEDMVAAQIPYDVQYSDIDYMERQLDFTLSPKFDGFPALINRMKANGMRVILILDPAISGNETKPYPPFTRGVEDDVFIKYPNDGSIVWGKVWPDFPDIFVNSSLDWDSQVEQYRAYVAFPDFFRNSTITWWKRELRELYTNPQDPEKSLKFDGMWIDMNEPSSFVNGAVSPGCRDSSLNHPPYMPYLESRNSGLSSKTLCMEGEQILPDGSRVRHYDVHSLYGWSQTRPTYEVVQEVTGERGIIISRSTYPSSGRWSGHWLGDNTAAWDQLRKSIIGMMEFSLFGISYTGADICGFFQDAEFEMCARWMQLGAFYPFSRNHNSIGTRRQDPVSWNDTFVNISRSVLETRYTLLPYLYTLMHMAHTEGSTVVRALLHEFVSDRVTWDLDSQFLLGPAFLVSPVLEPNARNVTAYFPRARWYDYYTGVDINARGEWRDLSAPLDHINLHIRGGYILPWQEPAQNTYFSRQKFMGFKVALDDDGTAEGWLFWDDGQSIDTYEQGLYYLANFSVSQNTMQSHVIFNKYISDANPLKLGYIEIWGVGSAPISSVSISASGEVITPIFIHDSATQVLNINVTNGNLSLHNFSSLTWTSAPDS

Entity 2 branched

描述 description	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ;
分子量 formula_weight	807.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	8

Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	570.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

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7. 引用文献 (1)

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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	2.77 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	607435

fit	/app/data/saxs_computation/kz/9kz7/9kz7.fit
pddf	/app/data/pr_computation/kz/9kz7/9kz7.pr.out
profile	/app/data/saxs_computation/kz/9kz7/9kz7.dat

The cryo-EM structure of porcine serum MGAM bound with Acarviosyl-maltotriose.

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

冷冻电镜 EM 3D