SAXSdb — 1ppm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ppm
沉积日期 deposition_date	1992-06-01
结构标题 title	CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES
关键词 keywords	ACID PROTEINASE, HYDROLASE-hydrolase inhibitor complex; HYDROLASE/hydrolase inhibitor
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	20.26 Å
回转半径 Rg (电子) rg_electron	19.28 Å
零角强度 I(0) i0	38977600.00
分子量 molecular_weight	32174.0 kDa
排除体积 excluded_volume	30983 Å³
包络体积 envelope_volume	48092 Å³
水化壳体积 shell_volume	20822 Å³
包络直径 envelope_diameter	67.2 Å
壳层 Rg shell_rg	25.84 Å
包络 Rg envelope_rg	19.44 Å
形状 Rg shape_rg	19.22 Å
总 Rg total_rg	20.02 Å
总原子数 total_atoms	2433
残基数 n_residues	323
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	65.2 Å
Rg (实空间) rg_real	20.18 Å
Rg 误差 (实空间) rg_real_error	0.30 Å
I(0) (实空间) i0_real	3.8980e+07
I(0) 误差 (实空间) i0_real_error	4.2490e+05
Rg (倒空间) rg_reciprocal	20.20 Å
I(0) (倒空间) i0_reciprocal	38980000.0000
解质量估计 total_estimate	0.8949
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	24.2 Å
偏度 Skewness skewness	0.245
峰度 Kurtosis kurtosis	-0.412
角度范围 angular_range	— – 0.3900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7316000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.995

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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 (6)

Entity 1 polymer

描述 description	PENICILLOPEPSIN
分子量 formula_weight	33468.8 kDa
EC 编号 ec_number	3.4.23.20
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	E
原子数 atom_count	2739

AASGVATNTPTANDEEYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFSSINTVQPQSQTTFFDTVKSSLAQPLFAVALKHQQPGVYDFGFIDSSKYTGSLTYTGVDNSQGFWSFNVDSYTAGSQSGDGFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGGIQSNSGIGFSIFGDIFLKSQYVVFDSDGPQLGFAPQA

来源 Source

来源生物 organism	Penicillium janthinellum
NCBI 分类编号 ncbi_taxonomy_id	5079

Entity 2 non-polymer

描述 description	;N-[(benzyloxy)carbonyl]-L-alanyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl }-L-alaninamide ;
分子量 formula_weight	605.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

描述 description	alpha-L-arabinopyranose
分子量 formula_weight	150.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	306

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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	d1ppme_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.50 — Acid proteases
超家族 Superfamily superfamily	b.50.1 — Acid proteases
家族 Family family	b.50.1.2 — Pepsin-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1ppmE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1ppmE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

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7. 引用文献 (12)

Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.

Biochemistry (1992)

PMID: 1606144 · DOI: 10.1021/bi00137a016 PRIMARY

Aspartic Proteinases and Their Catalytic Pathway

Biological Macromolecules and Assemblies (1987)

Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin

Biochemistry (1985)

Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution

J.Mol.Biol. (1983)

Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin

Proc.Natl.Acad.Sci.USA (1982)

The Tertiary Structure of Penicillopepsin. Towards a Catalytic Mechanism for Acid Proteases

STRUCTURAL STUDIES ON MOLECULES OF BIOLOGICA INTERESTL (1981)

An X-Ray Crystallographic Approach to Enzyme Structure and Function

Can.J.Biochem. (1980)

Structural Evidence for Gene Duplication in the Evolution of the Acid Proteases

Nature (1978)

Penicillopepsin. 2.8 Angstroms Structure, Active Site Conformation and Mechanistic Implications

Adv.Exp.Med.Biol. (1977)

Mechanism of Acid Protease Catalysis Based on the Crystal Structure of Penicillopepsin

Nature (1977)

Penicillopepsin from Penicillium Janthinellum Crystal Structure at 2.8 Angstroms and Sequence Homology with Porcine Pepsin

Nature (1977)

The Crystal Structure of Penicillopepsin at 6 Angstroms Resolution

Biochem.Biophys.Res.Commun. (1976)

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晶胞边长 a length_a	97.400 Å
晶胞边长 b length_b	46.590 Å
晶胞边长 c length_c	66.290 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	115.70 °
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	1.700 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.1500
R_work r_work	0.1500
R_free r_free	—

fit	/app/data/saxs_computation/pp/1ppm/1ppm.fit
pddf	/app/data/pr_computation/pp/1ppm/1ppm.pr.out
profile	/app/data/saxs_computation/pp/1ppm/1ppm.dat

CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution