SAXSdb — 2ejf

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ejf
沉积日期 deposition_date	2007-03-16
结构标题 title	;Crystal Structure Of The Biotin Protein Ligase (Mutations R48A and K111A) and Biotin Carboxyl Carrier Protein Complex From Pyrococcus Horikoshii OT3 ;
关键词 keywords	;Biotinylation, Dimer, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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	30.05 Å
回转半径 Rg (电子) rg_electron	29.46 Å
零角强度 I(0) i0	66348600.00
分子量 molecular_weight	67202.0 kDa
排除体积 excluded_volume	85789 Å³
包络体积 envelope_volume	104330 Å³
水化壳体积 shell_volume	30646 Å³
包络直径 envelope_diameter	110.9 Å
壳层 Rg shell_rg	35.25 Å
包络 Rg envelope_rg	29.64 Å
形状 Rg shape_rg	29.45 Å
总 Rg total_rg	30.09 Å
总原子数 total_atoms	4722
残基数 n_residues	600
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	105.6 Å
Rg (实空间) rg_real	30.20 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	6.6350e+07
I(0) 误差 (实空间) i0_real_error	1.0660e+06
Rg (倒空间) rg_reciprocal	30.14 Å
I(0) (倒空间) i0_reciprocal	66350000.0000
解质量估计 total_estimate	0.6538
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	27.9 Å
偏度 Skewness skewness	0.459
峰度 Kurtosis kurtosis	-0.332
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15730000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.838; Smooth: 0.992

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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 (6)

Entity 1 polymer

描述 description	235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
分子量 formula_weight	25959.3 kDa
突变 mutation	R48A/K111A
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	5131

MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGALNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKAIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVSLRFL

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 polymer

描述 description	149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
分子量 formula_weight	7985.5 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	C,D

MVVSENVVSAPMPGKVLRVLVRVGDRVRVGQGLLVLEAMKMENEIPSPRDGVVKRILVKEGEAVDTGQPLIELG

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 3 non-polymer

描述 description	BIOTIN
分子量 formula_weight	244.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	ADENOSINE
分子量 formula_weight	267.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	1

Entity 6 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	409

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2ejfa1
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	d2ejfa2
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	d2ejfb1
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	d2ejfb2
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 (6 domains)

结构域编号 domain_id	2ejfA01
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	2ejfA02
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	2ejfB01
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	2ejfB02
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	2ejfC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	2ejfD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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7. 引用文献 (1)

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晶胞边长 a length_a	69.849 Å
晶胞边长 b length_b	63.117 Å
晶胞边长 c length_c	75.636 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.86 °
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	37.620 Å
R 因子 r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2450

fit	/app/data/saxs_computation/ej/2ejf/2ejf.fit
pddf	/app/data/pr_computation/ej/2ejf/2ejf.pr.out
profile	/app/data/saxs_computation/ej/2ejf/2ejf.dat

;Crystal Structure Of The Biotin Protein Ligase (Mutations R48A and K111A) and Biotin Carboxyl Carrier Protein Complex From Pyrococcus Horikoshii OT3 ;

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

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)