1m9y

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex.

Method: X-RAY DIFFRACTION D_max: 152.5 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	1m9y
沉积日期 deposition_date	2002-07-30
结构标题 title	X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex.
关键词 keywords	CAPSID, HIV-1, CYCLOPHILIN A, ROTAMASE, Isomerase-Viral protein COMPLEX; Isomerase/Viral 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	44.98 Å
回转半径 Rg (电子) rg_electron	45.20 Å
零角强度 I(0) i0	270598000.00
分子量 molecular_weight	133910.0 kDa
排除体积 excluded_volume	167240 Å³
包络体积 envelope_volume	248510 Å³
水化壳体积 shell_volume	48099 Å³
包络直径 envelope_diameter	154.3 Å
壳层 Rg shell_rg	47.72 Å
包络 Rg envelope_rg	43.11 Å
形状 Rg shape_rg	45.19 Å
总 Rg total_rg	45.36 Å
总原子数 total_atoms	9408
残基数 n_residues	1220
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	152.5 Å
Rg (实空间) rg_real	45.17 Å
Rg 误差 (实空间) rg_real_error	1.95 Å
I(0) (实空间) i0_real	2.7060e+08
I(0) 误差 (实空间) i0_real_error	5.1860e+06
Rg (倒空间) rg_reciprocal	44.98 Å
I(0) (倒空间) i0_reciprocal	270500000.0000
解质量估计 total_estimate	0.8593
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	52.3 Å
偏度 Skewness skewness	0.342
峰度 Kurtosis kurtosis	-0.499
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9372000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.735

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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	Cyclophilin A
分子量 formula_weight	18036.5 kDa
EC 编号 ec_number	5.2.1.8
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,E,F
原子数 atom_count	10531

MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

来源 Source

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 BL21(DE3)

Entity 2 polymer

描述 description	HIV-1 Capsid
分子量 formula_weight	16151.5 kDa
突变 mutation	H87A,G89A
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	C,D,G,H

PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVAAAPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI 分类编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	1123

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1m9ya_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.62 — Cyclophilin-like
超家族 Superfamily superfamily	b.62.1 — Cyclophilin-like
家族 Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

结构域编号 domain_id	d1m9yb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.62 — Cyclophilin-like
超家族 Superfamily superfamily	b.62.1 — Cyclophilin-like
家族 Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

结构域编号 domain_id	d1m9yc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
超家族 Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
家族 Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

结构域编号 domain_id	d1m9yd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
超家族 Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
家族 Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

结构域编号 domain_id	d1m9ye_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.62 — Cyclophilin-like
超家族 Superfamily superfamily	b.62.1 — Cyclophilin-like
家族 Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

结构域编号 domain_id	d1m9yf_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.62 — Cyclophilin-like
超家族 Superfamily superfamily	b.62.1 — Cyclophilin-like
家族 Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

结构域编号 domain_id	d1m9yg_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
超家族 Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
家族 Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

结构域编号 domain_id	d1m9yh_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
超家族 Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
家族 Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1m9yA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	100 — Cyclophilin
同源超家族 H-superfamily homologous superfamily	10 — Cyclophilin-like

结构域编号 domain_id	1m9yB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	100 — Cyclophilin
同源超家族 H-superfamily homologous superfamily	10 — Cyclophilin-like

结构域编号 domain_id	1m9yC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
同源超家族 H-superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

结构域编号 domain_id	1m9yD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
同源超家族 H-superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

结构域编号 domain_id	1m9yE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	100 — Cyclophilin
同源超家族 H-superfamily homologous superfamily	10 — Cyclophilin-like

结构域编号 domain_id	1m9yF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	100 — Cyclophilin
同源超家族 H-superfamily homologous superfamily	10 — Cyclophilin-like

结构域编号 domain_id	1m9yG00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
同源超家族 H-superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

结构域编号 domain_id	1m9yH00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
同源超家族 H-superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

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7. 引用文献 (1)

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晶胞边长 a length_a	38.426 Å
晶胞边长 b length_b	111.223 Å
晶胞边长 c length_c	67.780 Å
晶胞夹角 α angle_alpha	89.99 °
晶胞夹角 β angle_beta	101.45 °
晶胞夹角 γ angle_gamma	89.75 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	19.690 Å
R 因子 r_factor	0.1691
R_work r_work	0.1620
R_free r_free	0.2342

fit	/app/data/saxs_computation/m9/1m9y/1m9y.fit
pddf	/app/data/pr_computation/m9/1m9y/1m9y.pr.out
profile	/app/data/saxs_computation/m9/1m9y/1m9y.dat

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex.

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)