SAXSdb — 2ffj

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ffj
沉积日期 deposition_date	2005-12-19
结构标题 title	CRYSTAL STRUCTURE OF a DUF89 family protein (AF1104) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 2.45 A RESOLUTION
关键词 keywords	STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	26.14 Å
回转半径 Rg (电子) rg_electron	25.32 Å
零角强度 I(0) i0	58938200.00
分子量 molecular_weight	59066.0 kDa
排除体积 excluded_volume	73658 Å³
包络体积 envelope_volume	88790 Å³
水化壳体积 shell_volume	29266 Å³
包络直径 envelope_diameter	87.3 Å
壳层 Rg shell_rg	32.71 Å
包络 Rg envelope_rg	25.36 Å
形状 Rg shape_rg	25.32 Å
总 Rg total_rg	26.14 Å
总原子数 total_atoms	4107
残基数 n_residues	531
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	84.3 Å
Rg (实空间) rg_real	26.16 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	5.8940e+07
I(0) 误差 (实空间) i0_real_error	8.4860e+05
Rg (倒空间) rg_reciprocal	26.16 Å
I(0) (倒空间) i0_reciprocal	58940000.0000
解质量估计 total_estimate	0.8899
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	29.0 Å
偏度 Skewness skewness	0.407
峰度 Kurtosis kurtosis	-0.302
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19940000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.927

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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	conserved hypothetical protein
分子量 formula_weight	33766.9 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	A,B
原子数 atom_count	4196

MGSDKIHHHHHHMKISPLCPSCLLGRVYYEAKLVTDDEDLISQCVDESLKILAENYSSRPINAHLATRIHRRVYEILGVEDPYAEVKARANEVARQVLPLAKEIVEGSDDPFKTAVIVSIVGNNFDYGVQGHKVVEEEFRDFLKRKVQEGLKINDTERIKELSSGKVVYLTDNAGEIFFDTLLMKEIKRRCEKLTAVVRGRPIISDATIEDARLARVDKIADELLTNGKGAIGIIMDELPDETRKALEEADLIVAKGMANYECLSDGSLKPIAFLLTAKCEPVARDIGVNVGDMVAKVVE

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	224325
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	89

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2ffja1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.50 — AF1104-like
超家族 Superfamily superfamily	e.50.1 — AF1104-like
家族 Family family	e.50.1.1 — AF1104-like

结构域编号 domain_id	d2ffjb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.50 — AF1104-like
超家族 Superfamily superfamily	e.50.1 — AF1104-like
家族 Family family	e.50.1.1 — AF1104-like

CATH v4.4 (6 domains)

结构域编号 domain_id	2ffjA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	380 — Uncharacterised protein PF01937, DUF89, domain 1

结构域编号 domain_id	2ffjA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 — Uncharacterised protein PF01937, DUF89, domain 2

结构域编号 domain_id	2ffjA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10880 — Uncharacterised protein PF01937, DUF89, domain 3

结构域编号 domain_id	2ffjB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	380 — Uncharacterised protein PF01937, DUF89, domain 1

结构域编号 domain_id	2ffjB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 — Uncharacterised protein PF01937, DUF89, domain 2

结构域编号 domain_id	2ffjB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10880 — Uncharacterised protein PF01937, DUF89, domain 3

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7. 引用文献 (1)

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晶胞边长 a length_a	68.806 Å
晶胞边长 b length_b	80.677 Å
晶胞边长 c length_c	120.868 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.450 Å
最低分辨率 resolution_low	29.900 Å
R 因子 r_factor	0.1919
R_work r_work	0.1890
R_free r_free	0.2550

fit	/app/data/saxs_computation/ff/2ffj/2ffj.fit
pddf	/app/data/pr_computation/ff/2ffj/2ffj.pr.out
profile	/app/data/saxs_computation/ff/2ffj/2ffj.dat

CRYSTAL STRUCTURE OF a DUF89 family protein (AF1104) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 2.45 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