SAXSdb — 2j4w

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2j4w
沉积日期 deposition_date	2006-09-07
结构标题 title	Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex
关键词 keywords	;IMMUNOGLOBULIN DOMAIN, IMMUNOGLOBULIN C REGION, MEMBRANE, TRANSMEMBRANE, HYPOTHETICAL PROTEIN, ANTIBODY CROSS-REACTIVITY, SURFACE ACTIVE PROTEIN, MALARIA VACCINE CANDIDATE, APICAL MEMBRANE ANTIGEN 1, IMMUNE SYSTEM ;; IMMUNE SYSTEM
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	26.38 Å
回转半径 Rg (电子) rg_electron	25.48 Å
零角强度 I(0) i0	46231400.00
分子量 molecular_weight	51342.0 kDa
排除体积 excluded_volume	63548 Å³
包络体积 envelope_volume	79764 Å³
水化壳体积 shell_volume	26570 Å³
包络直径 envelope_diameter	90.6 Å
壳层 Rg shell_rg	32.17 Å
包络 Rg envelope_rg	25.41 Å
形状 Rg shape_rg	25.44 Å
总 Rg total_rg	26.31 Å
总原子数 total_atoms	3606
残基数 n_residues	461
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	87.8 Å
Rg (实空间) rg_real	26.43 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	4.6230e+07
I(0) 误差 (实空间) i0_real_error	6.9290e+05
Rg (倒空间) rg_reciprocal	26.42 Å
I(0) (倒空间) i0_reciprocal	46230000.0000
解质量估计 total_estimate	0.8844
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	27.8 Å
偏度 Skewness skewness	0.387
峰度 Kurtosis kurtosis	-0.344
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9112000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.912

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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	APICAL MEMBRANE ANTIGEN 1
分子量 formula_weight	51361.9 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D
原子数 atom_count	3773

PTVERSTRMGNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFVMAGDQNSNYRHPAVYDEKEKTCHMLYLSAQENMGPRYCSPDAQNRDAVFCFKPDKDESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPTQYEEEMTDYQKIQQGFRQNNREMIKGAFLPVGAFNSDNFKSKGRGFNWANFDSVKRKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQSRNMNLYSVDGERIVLPRIFISNDKESIKCPCEPERISESTCNFYVCNCVEKRAEIKELNQVVIKEEFRLYYELGEEKSNKQMLL

来源 Source

来源生物 organism	PLASMODIUM VIVAX
NCBI 分类编号 ncbi_taxonomy_id	5855
宿主生物 host_organism	PICHIA PASTORIS

Entity 2 polymer

描述 description	FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
分子量 formula_weight	24189.0 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	H

EVQLVESGGGLVKPGGSLKLSCAASGFIFSDYYMYWVRQTPEKRLEWVATISDGNSYTYYVDSVKGRFTISRDNAKNNLYLQMSSLKSEDTAIYYCARDGPTDSSGYGGFGYWGQGTLVTVSEAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Entity 3 polymer

描述 description	FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
分子量 formula_weight	23285.6 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	L

QSVLSQSPAILSASPGEKVTMTCRARSSVSYMHWYQQKSGSSPKPWIHATSNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSHPPTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

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	155

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2j4wd1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.61 — Apical membrane antigen 1
超家族 Superfamily superfamily	g.61.1 — Apical membrane antigen 1
家族 Family family	g.61.1.1 — Apical membrane antigen 1

结构域编号 domain_id	d2j4wh1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2j4wh2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d2j4wl1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.0 — automated matches

结构域编号 domain_id	d2j4wl2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

结构域编号 domain_id	2j4wH01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2j4wH02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2j4wL01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2j4wL02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (2)

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晶胞边长 a length_a	171.787 Å
晶胞边长 b length_b	171.787 Å
晶胞边长 c length_c	44.748 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	6

空间群 space_group	P 63
空间群编号 int_tables_number	173
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1900
R_work r_work	0.1870
R_free r_free	0.2410

fit	/app/data/saxs_computation/j4/2j4w/2j4w.fit
pddf	/app/data/pr_computation/j4/2j4w/2j4w.pr.out
profile	/app/data/saxs_computation/j4/2j4w/2j4w.dat

Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.12.19 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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)