1tfm

CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM

Method: X-RAY DIFFRACTION D_max: 85.0 Å Quality: REASONABLE

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	1tfm
沉积日期 deposition_date	2004-05-27
结构标题 title	CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM
关键词 keywords	PROTEIN-INHIBITOR COMPLEX, BETA TREFOIL, Ribosome inactivating protein, TOXIN; TOXIN
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	26.16 Å
回转半径 Rg (电子) rg_electron	25.29 Å
零角强度 I(0) i0	56024000.00
分子量 molecular_weight	56812.0 kDa
排除体积 excluded_volume	70483 Å³
包络体积 envelope_volume	85065 Å³
水化壳体积 shell_volume	28523 Å³
包络直径 envelope_diameter	86.8 Å
壳层 Rg shell_rg	32.04 Å
包络 Rg envelope_rg	25.39 Å
形状 Rg shape_rg	25.28 Å
总 Rg total_rg	26.03 Å
总原子数 total_atoms	3995
残基数 n_residues	495
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	85.0 Å
Rg (实空间) rg_real	26.18 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	5.6020e+07
I(0) 误差 (实空间) i0_real_error	8.4960e+05
Rg (倒空间) rg_reciprocal	26.18 Å
I(0) (倒空间) i0_reciprocal	56020000.0000
解质量估计 total_estimate	0.7124
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	0.375
峰度 Kurtosis kurtosis	-0.396
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	12100000.0000
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: 0.885; Stabil: 1.000; Sysdev: 0.221; Positv: 1.000; Valcen: 0.984; Smooth: 0.957

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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 (10)

Entity 1 polymer

描述 description	Himalayan mistletoe ribosome-inactivating protein
分子量 formula_weight	26566.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4101

YERLDLDVTSQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSGGGVEAARFVLVELTNEGGDSITAAIDVTNLYVVAYQAGSQSYFLSGPGTHLFTGTTRSSLPFNGSYPDLEQYAGHRKQIPLGIDQLIQSVTALRFPGNTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQQSTEGVFNNPIRLAIPGNFVTLTNVRDVIASLAIMLFVC

Entity 2 polymer

描述 description	Himalayan mistletoe ribosome-inactivating protein
分子量 formula_weight	27633.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

CSASEPTVRIVGRNGMNVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWQIWGNGTIINPRSNLALAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFNDLCMESNGGSVWVETCVSQQNDRWALYGDGSIRPEQNQDQCLTSGRDSVAGINIVSCSGGSSGQRWVFTNEGAILNLKNGLAMDVANPGLGQIIIYPATGKPNQMWLPVP

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 branched

描述 description	beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	2-AMINO-4-ISOPROPYL-PTERIDINE-6-CARBOXYLIC ACID
分子量 formula_weight	233.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	beta-D-galactopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 10 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	106

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1tfma_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.165 — Ribosome inactivating proteins (RIP)
超家族 Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
家族 Family family	d.165.1.1 — Plant cytotoxins

结构域编号 domain_id	d1tfmb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.2 — Ricin B-like lectins
家族 Family family	b.42.2.1 — Ricin B-like

结构域编号 domain_id	d1tfmb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.2 — Ricin B-like lectins
家族 Family family	b.42.2.1 — Ricin B-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1tfmA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	420 — Ricin (A subunit); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

结构域编号 domain_id	1tfmA02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	470 — Ricin (A Subunit), domain 2
同源超家族 H-superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

结构域编号 domain_id	1tfmB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1tfmB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

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7. 引用文献 (1)

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晶胞边长 a length_a	109.422 Å
晶胞边长 b length_b	109.422 Å
晶胞边长 c length_c	309.798 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2400
R_work r_work	0.2343
R_free r_free	0.2886

fit	/app/data/saxs_computation/tf/1tfm/1tfm.fit
pddf	/app/data/pr_computation/tf/1tfm/1tfm.pr.out
profile	/app/data/saxs_computation/tf/1tfm/1tfm.dat

CRYSTAL STRUCTURE OF A RIBOSOME INACTIVATING PROTEIN IN ITS NATURALLY INHIBITED FORM

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 (10)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 branched

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)