8i8f

Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1

Method: X-RAY DIFFRACTION D_max: 80.1 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	8i8f
沉积日期 deposition_date	2023-02-04
结构标题 title	Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1
关键词 keywords	penicillin, hydrolase-inhibitor complex, HYDROLASE-INHIBITOR; HYDROLASE-INHIBITOR
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	24.48 Å
回转半径 Rg (电子) rg_electron	24.10 Å
零角强度 I(0) i0	47413600.00
分子量 molecular_weight	51781.0 kDa
排除体积 excluded_volume	64045 Å³
包络体积 envelope_volume	73906 Å³
水化壳体积 shell_volume	26032 Å³
包络直径 envelope_diameter	81.7 Å
壳层 Rg shell_rg	30.92 Å
包络 Rg envelope_rg	24.17 Å
形状 Rg shape_rg	24.15 Å
总 Rg total_rg	24.68 Å
总原子数 total_atoms	3670
残基数 n_residues	479
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	80.1 Å
Rg (实空间) rg_real	24.54 Å
Rg 误差 (实空间) rg_real_error	0.51 Å
I(0) (实空间) i0_real	4.7410e+07
I(0) 误差 (实空间) i0_real_error	6.8080e+05
Rg (倒空间) rg_reciprocal	24.53 Å
I(0) (倒空间) i0_reciprocal	47410000.0000
解质量估计 total_estimate	0.8795
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	25.4 Å
偏度 Skewness skewness	0.429
峰度 Kurtosis kurtosis	-0.334
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17650000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.958

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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 (4)

Entity 1 polymer

描述 description	Metallo beta lactamase NDM-1
分子量 formula_weight	28527.4 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,B
原子数 atom_count	4269

MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

来源 Source

来源生物 organism	Klebsiella pneumoniae
NCBI 分类编号 ncbi_taxonomy_id	573
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	;(2R,4S)-5,5-dimethyl-2-[(1R)-1-(2-naphthalen-1-yloxyethanoylamino)-2-oxidanyl-2-oxidanylidene-ethyl]-1,3-thiazolidine-4-carboxylic acid ;
分子量 formula_weight	418.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	558

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7. 引用文献 (1)

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晶胞边长 a length_a	39.114 Å
晶胞边长 b length_b	78.847 Å
晶胞边长 c length_c	133.534 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.890 Å
最低分辨率 resolution_low	27.770 Å
R 因子 r_factor	0.1529
R_work r_work	0.1510
R_free r_free	0.1895

fit	/app/data/saxs_computation/i8/8i8f/8i8f.fit
pddf	/app/data/pr_computation/i8/8i8f/8i8f.pr.out
profile	/app/data/saxs_computation/i8/8i8f/8i8f.dat

Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1

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