2awa

;Crystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) (np_344555.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 2.50 A resolution ;

Method: X-RAY DIFFRACTION D_max: 129.3 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	2awa
沉积日期 deposition_date	2005-08-31
结构标题 title	;Crystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) (np_344555.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 2.50 A resolution ;
关键词 keywords	;np_344555.1, DNA polymerase III, beta chain (EC 2.7.7.7), Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, 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	41.71 Å
回转半径 Rg (电子) rg_electron	41.12 Å
零角强度 I(0) i0	367889000.00
分子量 molecular_weight	161700.0 kDa
排除体积 excluded_volume	204520 Å³
包络体积 envelope_volume	299990 Å³
水化壳体积 shell_volume	61378 Å³
包络直径 envelope_diameter	130.5 Å
壳层 Rg shell_rg	46.65 Å
包络 Rg envelope_rg	39.47 Å
形状 Rg shape_rg	41.12 Å
总 Rg total_rg	41.46 Å
总原子数 total_atoms	11387
残基数 n_residues	1497
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	129.3 Å
Rg (实空间) rg_real	41.56 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	3.6790e+08
I(0) 误差 (实空间) i0_real_error	6.4020e+06
Rg (倒空间) rg_reciprocal	41.71 Å
I(0) (倒空间) i0_reciprocal	367900000.0000
解质量估计 total_estimate	0.8825
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	54.5 Å
偏度 Skewness skewness	0.146
峰度 Kurtosis kurtosis	-0.475
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25360000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.778

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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	DNA polymerase III, beta chain
分子量 formula_weight	43763.7 kDa
EC 编号 ec_number	2.7.7.7
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	11638

MGSDKIHHHHHHMIHFSINKNLFLQALNTTKRAISSKNAIPILSTVKIDVTNEGITLIGSNGQISIENFISQKNEDAGLLITSLGSILLEASFFINVVSSLPDVTLDFKEIEQNQIVLTSGKSEITLKGKDSEQYPRIQEISASTPLILETKLLKKIINETAFAASTQESRPILTGVHFVLSQHKELKTVATDSHRLSQKKLTLEKNSDDFDVVIPSRSLREFSAVFTDDIETVEIFFANNQILFRSENISFYTRLLEGNYPDTDRLIPTDFNTTITFNVVNLRQSMERARLLSSATQNGTVKLEIKDGVVSAHVHSPEVGKVNEEIDTDQVTGEDLTISFNPTYLIDSLKALNSEKVTISFISAVRPFTLVPADTDEDFMQLITPVRTN

来源 Source

来源生物 organism	Streptococcus pneumoniae
NCBI 分类编号 ncbi_taxonomy_id	170187
宿主生物 host_organism	Escherichia coli

Entity 2 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 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	251

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2awaA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	2awaA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	70 — Box
拓扑 Topology topology	10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2awaB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	2awaB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	70 — Box
拓扑 Topology topology	10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2awaC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	2awaC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	70 — Box
拓扑 Topology topology	10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2awaD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	2awaD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	70 — Box
拓扑 Topology topology	10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	94.060 Å
晶胞边长 b length_b	70.720 Å
晶胞边长 c length_c	135.440 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.04 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.500 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.1920
R_free r_free	0.2500

fit	/app/data/saxs_computation/aw/2awa/2awa.fit
pddf	/app/data/pr_computation/aw/2awa/2awa.pr.out
profile	/app/data/saxs_computation/aw/2awa/2awa.dat

;Crystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) (np_344555.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 2.50 A resolution ;

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