SAXSdb — 1x01

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1x01
沉积日期 deposition_date	2005-03-11
结构标题 title	Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Ot3 in complex with ATP
关键词 keywords	;Biotin Protein Ligase, Dimer, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, NPPSFA, National Project on Protein Structural and Functional Analyses, LIGASE ;; LIGASE
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	28.02 Å
回转半径 Rg (电子) rg_electron	27.54 Å
零角强度 I(0) i0	43751600.00
分子量 molecular_weight	53439.0 kDa
排除体积 excluded_volume	67864 Å³
包络体积 envelope_volume	80203 Å³
水化壳体积 shell_volume	26144 Å³
包络直径 envelope_diameter	110.9 Å
壳层 Rg shell_rg	32.33 Å
包络 Rg envelope_rg	27.98 Å
形状 Rg shape_rg	27.51 Å
总 Rg total_rg	28.12 Å
总原子数 total_atoms	3753
残基数 n_residues	470
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	104.7 Å
Rg (实空间) rg_real	28.43 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	4.3750e+07
I(0) 误差 (实空间) i0_real_error	6.8920e+05
Rg (倒空间) rg_reciprocal	28.30 Å
I(0) (倒空间) i0_reciprocal	43750000.0000
解质量估计 total_estimate	0.5442
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.7 Å
偏度 Skewness skewness	0.676
峰度 Kurtosis kurtosis	0.020
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12150000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.469; Stabil: 1.000; Sysdev: 0.075; Positv: 1.000; Valcen: 0.532; 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 (5)

Entity 1 polymer

描述 description	biotin--[acetyl-CoA-carboxylase] ligase
分子量 formula_weight	26103.5 kDa
EC 编号 ec_number	6.3.4.15
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	4090

MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGRLNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKKIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVSLRFL

来源 Source

来源生物 organism	Pyrococcus horikoshii
NCBI 分类编号 ncbi_taxonomy_id	70601
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 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	337

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1x01a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.1 — Biotin repressor (BirA)

结构域编号 domain_id	d1x01a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.104 — Class II aaRS and biotin synthetases
超家族 Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
家族 Family family	d.104.1.2 — Biotin holoenzyme synthetase

结构域编号 domain_id	d1x01b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
家族 Family family	b.34.1.1 — Biotin repressor (BirA)

结构域编号 domain_id	d1x01b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.104 — Class II aaRS and biotin synthetases
超家族 Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
家族 Family family	d.104.1.2 — Biotin holoenzyme synthetase

CATH v4.4 (4 domains)

结构域编号 domain_id	1x01A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	930 — BirA Bifunctional Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

结构域编号 domain_id	1x01A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1x01B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	930 — BirA Bifunctional Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

结构域编号 domain_id	1x01B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

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7. 引用文献 (1)

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晶胞边长 a length_a	38.404 Å
晶胞边长 b length_b	82.828 Å
晶胞边长 c length_c	72.174 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.78 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	32.390 Å
R 因子 r_factor	—
R_work r_work	0.1950
R_free r_free	0.2250

fit	/app/data/saxs_computation/x0/1x01/1x01.fit
pddf	/app/data/pr_computation/x0/1x01/1x01.pr.out
profile	/app/data/saxs_computation/x0/1x01/1x01.dat

Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Ot3 in complex with ATP

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