1z2i

CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

Method: X-RAY DIFFRACTION D_max: 137.2 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	1z2i
沉积日期 deposition_date	2005-03-08
结构标题 title	CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
关键词 keywords	;MALATE DEHYDROGENASE, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, New York SGX Research Center for Structural Genomics, NYSGXRC, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	39.36 Å
回转半径 Rg (电子) rg_electron	39.57 Å
零角强度 I(0) i0	373445000.00
分子量 molecular_weight	152270.0 kDa
排除体积 excluded_volume	188250 Å³
包络体积 envelope_volume	234770 Å³
水化壳体积 shell_volume	51488 Å³
包络直径 envelope_diameter	147.5 Å
壳层 Rg shell_rg	43.12 Å
包络 Rg envelope_rg	39.27 Å
形状 Rg shape_rg	39.59 Å
总 Rg total_rg	39.72 Å
总原子数 total_atoms	10700
残基数 n_residues	1400
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	137.2 Å
Rg (实空间) rg_real	39.79 Å
Rg 误差 (实空间) rg_real_error	1.36 Å
I(0) (实空间) i0_real	3.7340e+08
I(0) 误差 (实空间) i0_real_error	6.4300e+06
Rg (倒空间) rg_reciprocal	39.53 Å
I(0) (倒空间) i0_reciprocal	373300000.0000
解质量估计 total_estimate	0.8113
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	37.7 Å
偏度 Skewness skewness	0.575
峰度 Kurtosis kurtosis	-0.223
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	121400000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.663; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.720

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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 (3)

Entity 1 polymer

描述 description	malate dehydrogenase
分子量 formula_weight	38298.4 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	11399

MAHGNEKATVLARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH

来源 Source

来源生物 organism	Agrobacterium tumefaciens
NCBI 分类编号 ncbi_taxonomy_id	358
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	699

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1z2ia_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.122 — L-sulfolactate dehydrogenase-like
超家族 Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
家族 Family family	c.122.1.0 — automated matches

结构域编号 domain_id	d1z2ib_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.122 — L-sulfolactate dehydrogenase-like
超家族 Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
家族 Family family	c.122.1.0 — automated matches

结构域编号 domain_id	d1z2ic_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.122 — L-sulfolactate dehydrogenase-like
超家族 Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
家族 Family family	c.122.1.0 — automated matches

结构域编号 domain_id	d1z2id_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.122 — L-sulfolactate dehydrogenase-like
超家族 Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
家族 Family family	c.122.1.0 — automated matches

CATH v4.4 (12 domains)

结构域编号 domain_id	1z2iA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

结构域编号 domain_id	1z2iA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

结构域编号 domain_id	1z2iA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

结构域编号 domain_id	1z2iB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

结构域编号 domain_id	1z2iB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

结构域编号 domain_id	1z2iB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

结构域编号 domain_id	1z2iC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

结构域编号 domain_id	1z2iC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

结构域编号 domain_id	1z2iC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

结构域编号 domain_id	1z2iD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

结构域编号 domain_id	1z2iD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

结构域编号 domain_id	1z2iD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

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7. 引用文献 (1)

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晶胞边长 a length_a	98.220 Å
晶胞边长 b length_b	98.220 Å
晶胞边长 c length_c	146.470 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 31
空间群编号 int_tables_number	144
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2650

fit	/app/data/saxs_computation/z2/1z2i/1z2i.fit
pddf	/app/data/pr_computation/z2/1z2i/1z2i.pr.out
profile	/app/data/saxs_computation/z2/1z2i/1z2i.dat