9ozd

Crystal structure of the polysaccharide lyase RbmB from Vibrio cholerae bound to Vibrio Polysaccharide

Method: X-RAY DIFFRACTION D_max: 138.6 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	9ozd
沉积日期 deposition_date	2025-06-05
结构标题 title	Crystal structure of the polysaccharide lyase RbmB from Vibrio cholerae bound to Vibrio Polysaccharide
关键词 keywords	polysaccharide lyase, beta-helix, periplasm, glycosidase, LYASE; LYASE
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	41.36 Å
回转半径 Rg (电子) rg_electron	41.39 Å
零角强度 I(0) i0	449711000.00
分子量 molecular_weight	167690.0 kDa
排除体积 excluded_volume	206680 Å³
包络体积 envelope_volume	256480 Å³
水化壳体积 shell_volume	52800 Å³
包络直径 envelope_diameter	143.4 Å
壳层 Rg shell_rg	45.24 Å
包络 Rg envelope_rg	41.18 Å
形状 Rg shape_rg	41.37 Å
总 Rg total_rg	41.61 Å
总原子数 total_atoms	22979
残基数 n_residues	1467
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	138.6 Å
Rg (实空间) rg_real	41.56 Å
Rg 误差 (实空间) rg_real_error	1.50 Å
I(0) (实空间) i0_real	4.4970e+08
I(0) 误差 (实空间) i0_real_error	8.9570e+06
Rg (倒空间) rg_reciprocal	41.36 Å
I(0) (倒空间) i0_reciprocal	449600000.0000
解质量估计 total_estimate	0.8547
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	36.5 Å
偏度 Skewness skewness	0.446
峰度 Kurtosis kurtosis	-0.512
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	108700000.0000
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: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.727

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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 (8)

Entity 1 polymer

描述 description	Polysaccharide lyase
分子量 formula_weight	42697.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	25213

GSTEVNSHNVIEYGAIANDGEDDSNAFQHALNQLNNGDALIIPTGEYQICKTLYLKEKNNIEIIGSINSKLKKCRSFNGEYLLHITYTQNLKIQGLSFEGLNNGDLKPLWGEQGVYLGSTKGTLVVQNQFARFGDAALRMTTASQDHSIPPGSMAIKVSHNHFEDCAQVTTTQATAGTEMHGTQDIIIDNNQFNACKLKLSARADTRGAKVINNQFENINGTSNEVSYYSDVYYSGNTFLNINGFAINIYPNSRTEQNVQWGNISIIGNTFDAIQQGIRLQSFSINDPNNQSIKNIQISDNTFENIYFGNEIESQYKAIIRTNSQDNLVSFEHVNITGNQYQLTPYSKFISIDHKSKLINIQNNERIYSDHYYIQHFIKD

来源 Source

来源生物 organism	Vibrio cholerae
NCBI 分类编号 ncbi_taxonomy_id	948564
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose ;
分子量 formula_weight	760.6 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 branched

描述 description	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-{[(2R,3S,4R,5S,6R)-5-acetamido-3,4,6-trihydroxyoxane-2-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose ;
分子量 formula_weight	1197.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-{[(2R,3S,4R,5S,6R)-5-acetamido-3,4,6-trihydroxyoxane-2-carbonyl]amino}acetic acid (non-preferred name) ;
分子量 formula_weight	1034.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	13

Entity 7 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 8 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	1280

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7. 引用文献 (2)

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晶胞边长 a length_a	123.555 Å
晶胞边长 b length_b	52.563 Å
晶胞边长 c length_c	133.229 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.22 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.620 Å
最低分辨率 resolution_low	33.420 Å
R 因子 r_factor	0.1699
R_work r_work	0.1678
R_free r_free	0.2094

fit	/app/data/saxs_computation/oz/9ozd/9ozd.fit
pddf	/app/data/pr_computation/oz/9ozd/9ozd.pr.out
profile	/app/data/saxs_computation/oz/9ozd/9ozd.dat