SAXSdb — 1i1m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1i1m
沉积日期 deposition_date	2001-02-02
结构标题 title	CRYSTAL STRUCTURE OF ESCHERICHIA COLI BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE.
关键词 keywords	AMINOTRANSFERASE, HEXAMER, PLP, 4-METHYLVARELATE, TRANSFERASE; TRANSFERASE
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	32.26 Å
回转半径 Rg (电子) rg_electron	31.32 Å
零角强度 I(0) i0	163606000.00
分子量 molecular_weight	101480.0 kDa
排除体积 excluded_volume	126680 Å³
包络体积 envelope_volume	160990 Å³
水化壳体积 shell_volume	42467 Å³
包络直径 envelope_diameter	100.7 Å
壳层 Rg shell_rg	38.67 Å
包络 Rg envelope_rg	31.30 Å
形状 Rg shape_rg	31.32 Å
总 Rg total_rg	31.93 Å
总原子数 total_atoms	7155
残基数 n_residues	912
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	99.1 Å
Rg (实空间) rg_real	32.14 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	1.6360e+08
I(0) 误差 (实空间) i0_real_error	2.3330e+06
Rg (倒空间) rg_reciprocal	32.20 Å
I(0) (倒空间) i0_reciprocal	163600000.0000
解质量估计 total_estimate	0.9081
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	36.4 Å
偏度 Skewness skewness	0.200
峰度 Kurtosis kurtosis	-0.610
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	23100000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.904

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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	BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
分子量 formula_weight	34131.6 kDa
EC 编号 ec_number	2.6.1.42
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	7450

MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQVNQ

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	4-METHYL VALERIC ACID
分子量 formula_weight	116.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	295

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1i1ma_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

结构域编号 domain_id	d1i1mb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

结构域编号 domain_id	d1i1mc_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

CATH v4.4 (6 domains)

结构域编号 domain_id	1i1mA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	1i1mA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

结构域编号 domain_id	1i1mB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	1i1mB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

结构域编号 domain_id	1i1mC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	1i1mC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	155.990 Å
晶胞边长 b length_b	100.710 Å
晶胞边长 c length_c	141.530 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	24

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	—
R_work r_work	0.1730
R_free r_free	0.2150

fit	/app/data/saxs_computation/i1/1i1m/1i1m.fit
pddf	/app/data/pr_computation/i1/1i1m/1i1m.pr.out
profile	/app/data/saxs_computation/i1/1i1m/1i1m.dat

CRYSTAL STRUCTURE OF ESCHERICHIA COLI BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE.

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