SAXSdb — 2dqu

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2dqu
沉积日期 deposition_date	2006-05-30
结构标题 title	Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog
关键词 keywords	CATALYTIC ANTIBODY, ESTER HYDROLYSIS, ESTEROLYTIC, FAB, IMMUNOGLOBULIN, 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	26.10 Å
回转半径 Rg (电子) rg_electron	24.96 Å
零角强度 I(0) i0	40982300.00
分子量 molecular_weight	48704.0 kDa
排除体积 excluded_volume	60495 Å³
包络体积 envelope_volume	73780 Å³
水化壳体积 shell_volume	24982 Å³
包络直径 envelope_diameter	80.7 Å
壳层 Rg shell_rg	31.83 Å
包络 Rg envelope_rg	24.55 Å
形状 Rg shape_rg	24.93 Å
总 Rg total_rg	25.79 Å
总原子数 total_atoms	3422
残基数 n_residues	426
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	83.4 Å
Rg (实空间) rg_real	26.10 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	4.0980e+07
I(0) 误差 (实空间) i0_real_error	5.7030e+05
Rg (倒空间) rg_reciprocal	26.11 Å
I(0) (倒空间) i0_reciprocal	40980000.0000
解质量估计 total_estimate	0.9047
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	27.4 Å
偏度 Skewness skewness	0.281
峰度 Kurtosis kurtosis	-0.577
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	6026000.0000
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: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.955

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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	IMMUNOGLOBULIN 6D9
分子量 formula_weight	24101.7 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	L
原子数 atom_count	3679

DVLMTQTPLSLPVSLGDQASISCRSSQTIVHSNGDTYLDWFLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 2 polymer

描述 description	IMMUNOGLOBULIN 6D9
分子量 formula_weight	24134.2 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

EVKLVESGGGLVKPGGSLKLSCAASGFTFSNYAMSWVRQTPEKRLEWVVSISSGGSIYYLDSVKGRFTVSRDNARNILYLQMTSLRSEDTAMYFCARVSHYDGSRDWYFDVWGAGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Entity 3 non-polymer

描述 description	;[1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER ;
分子量 formula_weight	743.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	257

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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	d2dquh_
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	d2dqul1
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	d2dqul2
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	2dquH01
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	2dquH02
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	2dquL01
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	2dquL02
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 (8)

Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis

J.Mol.Biol. (2007)

PMID: 17428500 · DOI: 10.1016/j.jmb.2007.03.023 PRIMARY

;Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: evidence for an essential histidine involved in transition state stabilization ;

J.Mol.Biol. (1997)

PMID: 9150409 · DOI: 10.1006/jmbi.1997.0938

;Correlation between Antigen-Combining-Site Structures and Functions within a Panel of Catalytic Antibodies Generated against a Single Transition State Analog ;

J.Am.Chem.Soc. (1995)

DOI: 10.1021/ja00128a006

;Crystallization and Preliminary X-Ray Analysis: Transition State Complex of a Chloramphenicol Prodrug Activation Specific Catalytic Antibody ;

Protein Pept.Lett. (1995)

A common ancestry for multiple catalytic antibodies generated against a single transition-state analog

Proc.Natl.Acad.Sci.Usa (1994)

PMID: 7938025 · DOI: 10.1073/pnas.91.22.10757a

A common ancestry for multiple catalytic antibodies generated against a single transition-state analog

Proc.Natl.Acad.Sci.Usa (1994)

PMID: 8016113 · DOI: 10.1073/pnas.91.13.6045

Prodrug activation via catalytic antibodies

Proc.Natl.Acad.Sci.Usa (1993)

PMID: 8506382 · DOI: 10.1073/pnas.90.11.5337

Thermodynamic and Structural Analyses of Hydrolytic Mechanism by Catalytic Antibodies

To be Published

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晶胞边长 a length_a	58.700 Å
晶胞边长 b length_b	63.040 Å
晶胞边长 c length_c	56.560 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.75 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

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	1.700 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2460

fit	/app/data/saxs_computation/dq/2dqu/2dqu.fit
pddf	/app/data/pr_computation/dq/2dqu/2dqu.pr.out
profile	/app/data/saxs_computation/dq/2dqu/2dqu.dat

Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog

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

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 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 (8)

8. 文件与曲线 (10)

Files (7)

Curves (3)