SAXSdb — 1nf1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nf1
沉积日期 deposition_date	1998-07-08
结构标题 title	THE GAP RELATED DOMAIN OF NEUROFIBROMIN
关键词 keywords	;NEUROFIBROMIN, TYPE I NEUROFIBROMATOSIS, NF1, RAS, GAP, SIGNAL TRANSDUCTION, CANCER, GROWTH REGULATION, GTP HYDROLYSIS, PATIENT MUTATION, ARGININE FINGER, SIGNALING PROTEIN ;; SIGNALING PROTEIN
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	22.04 Å
回转半径 Rg (电子) rg_electron	21.20 Å
零角强度 I(0) i0	13166000.00
分子量 molecular_weight	27780.0 kDa
排除体积 excluded_volume	35052 Å³
包络体积 envelope_volume	43595 Å³
水化壳体积 shell_volume	18245 Å³
包络直径 envelope_diameter	77.2 Å
壳层 Rg shell_rg	26.81 Å
包络 Rg envelope_rg	21.53 Å
形状 Rg shape_rg	21.21 Å
总 Rg total_rg	22.04 Å
总原子数 total_atoms	1947
残基数 n_residues	259
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	74.2 Å
Rg (实空间) rg_real	22.18 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	1.3170e+07
I(0) 误差 (实空间) i0_real_error	2.1220e+05
Rg (倒空间) rg_reciprocal	22.15 Å
I(0) (倒空间) i0_reciprocal	13170000.0000
解质量估计 total_estimate	0.7720
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	65.3 Å
偏度 Skewness skewness	0.513
峰度 Kurtosis kurtosis	-0.203
角度范围 angular_range	— – 0.3600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4742000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.723; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.865; Smooth: 0.000

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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 (1)

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1nf1a_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.116 — GTPase activation domain, GAP
超家族 Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
家族 Family family	a.116.1.2 — p120GAP domain-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1nf1A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	506 — GTPase Activation - p120GAP; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GTPase Activation - p120gap; domain 1

结构域编号 domain_id	1nf1A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	506 — GTPase Activation - p120GAP; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GTPase Activation - p120gap; domain 1

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7. 引用文献 (11)

Structural analysis of the GAP-related domain from neurofibromin and its implications.

EMBO J. (1998)

PMID: 9687500 · DOI: 10.1093/emboj/17.15.4313 PRIMARY

The Ras-Rasgap Complex: Structural Basis for Gtpase Activation and its Loss in Oncogenic Ras Mutants

Science (1997)

DOI: 10.1126/science.277.5324.333

Confirmation of the Arginine-Finger Hypothesis for the Gap-Stimulated GTP- Hydrolysis Reaction of Ras

Nat.Struct.Biol. (1997)

Structural Differences in the Minimal Catalytic Domains of the Gtpasse- Activating Proteins P120Gap and Neurofibromin

J.Biol.Chem. (1996)

DOI: 10.1074/jbc.271.27.16409

3-Dimensional Structure of the Gtpase Activating Domain of Human P120Gap and Implications for the Interaction with Ras

Nature (1996)

DOI: 10.1038/384591a0

Formation of a Transition-State Analog of the Ras Gtpase Reaction by Ras:Gdp, Tetrafluoroaluminate and Gtpase-Activating Proteins

Science (1996)

The Neurofibromatosis Type I Gene and its Protein Product

Neuron (1993)

;Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 A Resolution: Implications for the Mechanism of GTP Hydrolysis ;

Embo J. (1990)

The NF1 Locus Encodes a Protein Functionally Related to Mammalian Gap and Yeast Ira Proteins

Cell(Cambridge,Mass.) (1990)

DOI: 10.1016/0092-8674(90)90151-4

The Gap-Related Domain of the Neurofibromatosis Type I Gene Product Interacts with Ras P21

Cell(Cambridge,Mass.) (1990)

DOI: 10.1016/0092-8674(90)90150-D

;The Catalytic Domain of the Neurofibromatosis Type I Gene Product Stimulates Ras Gtpase and Complements Ira Mutants of S. Cerevisiae ;

Cell(Cambridge,Mass.) (1990)

DOI: 10.1016/0092-8674(90)90149-9

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晶胞边长 a length_a	88.250 Å
晶胞边长 b length_b	58.300 Å
晶胞边长 c length_c	74.800 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	118.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
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	0.2660
R_work r_work	0.2660
R_free r_free	0.3690

描述 description	PROTEIN (NEUROFIBROMIN)
分子量 formula_weight	37982.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	1948

THE GAP RELATED DOMAIN OF NEUROFIBROMIN

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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. 引用文献 (11)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/nf/1nf1/1nf1.fit
pddf	/app/data/pr_computation/nf/1nf1/1nf1.pr.out
profile	/app/data/saxs_computation/nf/1nf1/1nf1.dat