SAXSdb — 1mrz

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mrz
沉积日期 deposition_date	2002-09-19
结构标题 title	Crystal structure of a flavin binding protein from Thermotoga Maritima, TM379
关键词 keywords	;Rossmann fold, flavin binding domain, 6-stranded beta barrel, nucleotide binding domain, Structural Genomics, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, 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	28.49 Å
回转半径 Rg (电子) rg_electron	27.60 Å
零角强度 I(0) i0	58374000.00
分子量 molecular_weight	61919.0 kDa
排除体积 excluded_volume	78612 Å³
包络体积 envelope_volume	101460 Å³
水化壳体积 shell_volume	30751 Å³
包络直径 envelope_diameter	99.1 Å
壳层 Rg shell_rg	34.85 Å
包络 Rg envelope_rg	27.47 Å
形状 Rg shape_rg	27.60 Å
总 Rg total_rg	28.39 Å
总原子数 total_atoms	4372
残基数 n_residues	536
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	93.3 Å
Rg (实空间) rg_real	28.43 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	5.8370e+07
I(0) 误差 (实空间) i0_real_error	8.0550e+05
Rg (倒空间) rg_reciprocal	28.45 Å
I(0) (倒空间) i0_reciprocal	58370000.0000
解质量估计 total_estimate	0.8986
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	31.7 Å
偏度 Skewness skewness	0.233
峰度 Kurtosis kurtosis	-0.524
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21210000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.980

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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	Riboflavin kinase/FMN adenylyltransferase
分子量 formula_weight	33665.8 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	4814

MVVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHKDREFGRKLGFPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPTVGDARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSKFEKEG

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CITRIC ACID
分子量 formula_weight	192.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	442

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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	d1mrza1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.5 — Riboflavin kinase-like
家族 Family family	b.43.5.1 — ATP-dependent riboflavin kinase-like

结构域编号 domain_id	d1mrza2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.3 — Adenylyltransferase

结构域编号 domain_id	d1mrzb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.5 — Riboflavin kinase-like
家族 Family family	b.43.5.1 — ATP-dependent riboflavin kinase-like

结构域编号 domain_id	d1mrzb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.3 — Adenylyltransferase

CATH v4.4 (4 domains)

结构域编号 domain_id	1mrzA01
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	620 — HUPs

结构域编号 domain_id	1mrzA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	30 — Riboflavin kinase-like

结构域编号 domain_id	1mrzB01
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	620 — HUPs

结构域编号 domain_id	1mrzB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	30 — Riboflavin kinase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	67.211 Å
晶胞边长 b length_b	83.095 Å
晶胞边长 c length_c	67.851 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	116.93 °
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	1.900 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2335

fit	/app/data/saxs_computation/mr/1mrz/1mrz.fit
pddf	/app/data/pr_computation/mr/1mrz/1mrz.pr.out
profile	/app/data/saxs_computation/mr/1mrz/1mrz.dat

Crystal structure of a flavin binding protein from Thermotoga Maritima, TM379

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