SAXSdb — 3lq0

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

ProAstacin

Astacus astacus

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 16–250	突变：I91L,E93A	ZN ZINC ION × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；For crystallization, reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Innovadyne) by a Cartesian (Genomic Solutions) nanodrop robot at the High-Throughput Crystallography Platform of the Barcelona Science Park. Best crystals appeared in a Bruker steady-temperature crystal farm at 4C with protein solution (10 mg/mL in 50mM AMPSO pH9.0) and 20% PEG 8000, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6 as reservoir solution. These conditions were efficiently scaled up to the microliter range with 24-well Cryschem crystallization dishes (Hampton Research). Crystals were cryo-protected with 16% PEG 8000, 20% glycerol, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6. , VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.45 Å R-free 0.180

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 3LQ0	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1AST STRUCTURE OF ASTACIN AND IMPLICATIONS FOR ACTIVATION OF ASTACINS AND ZINC-LIGATION OF COLLAGENASES 提交 1993-04-21	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–249（200 aa）	未记录	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.80 Å
1IAA CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY 提交 1994-05-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–249（200 aa）	未记录	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.90 Å
1IAB CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY 提交 1994-05-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–249（200 aa）	未记录	CO COBALT (II) ION × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.79 Å
1IAC REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-ENDOPEPTIDASE FROM THE CRAYFISH ASTACUS ASTACUS L. STRUCTURE DETERMINATION, REFINEMENT, MOLECULAR STRUCTURE AND COMPARISON WITH THERMOLYSIN 提交 1994-05-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–249（200 aa）	未记录	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.10 Å
1IAD REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-ENDOPEPTIDASE FROM THE CRAYFISH ASTACUS ASTACUS L. STRUCTURE DETERMINATION, REFINEMENT, MOLECULAR STRUCTURE AND COMPARISON TO THERMOLYSIN 提交 1994-05-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–249（200 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.30 Å
1IAE CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY 提交 1994-05-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–249（200 aa）	未记录	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.83 Å
1QJI Structure of astacin with a transition-state analogue inhibitor 提交 1999-06-24	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–249（200 aa）片段：CATALYTIC DOMAIN	未记录	ZN ZINC ION × 1 PKF CARBOBENZOXY-PRO-LYS-PHE-Y(PO2)-ALA-PRO-OME × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE	分辨率 2.14 Å
1QJJ Structure of astacin with a hydroxamic acid inhibitor 提交 1999-06-24	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 50–249（200 aa）片段：CATALYTIC DOMAIN	未记录	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE	分辨率 1.86 Å
6HT9 Mouse fetuin-B in complex with crayfish astacin 提交 2018-10-03	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 1–251（251 aa）	未记录	ZN ZINC ION × 1 GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6.	分辨率 3.10 Å R-free 0.270
6HT9 Mouse fetuin-B in complex with crayfish astacin 提交 2018-10-03	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 C 1–251（251 aa）	未记录	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6.	分辨率 3.10 Å R-free 0.270
6SAZ Cleaved human fetuin-b in complex with crayfish astacin 提交 2019-07-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 50–251（202 aa）	未记录	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.	分辨率 3.00 Å R-free 0.247
6SAZ Cleaved human fetuin-b in complex with crayfish astacin 提交 2019-07-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 其他组合异源复合物；蛋白 × 2 PDB 声明：dimeric	链 C 50–251（202 aa）	未记录	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.	分辨率 3.00 Å R-free 0.247

共 10 个其他 PDB 条目、12 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	ASTA_ASTFL
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–235； UniProt 16–250

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3lq0
沉积日期 deposition_date	2010-02-08
结构标题 title	Zymogen structure of crayfish astacin metallopeptidase
关键词 keywords	metallopeptidase, zymogen activation, proenzyme, protease, Disulfide bond, Hydrolase, Metal-binding, Metalloprotease, Zymogen; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	18.08 Å
回转半径 Rg (电子) rg_electron	17.00 Å
零角强度 I(0) i0	13671800.00
分子量 molecular_weight	26824.0 kDa
排除体积 excluded_volume	33096 Å³
包络体积 envelope_volume	36965 Å³
水化壳体积 shell_volume	17923 Å³
包络直径 envelope_diameter	59.1 Å
壳层 Rg shell_rg	23.54 Å
包络 Rg envelope_rg	17.34 Å
形状 Rg shape_rg	16.99 Å
总 Rg total_rg	17.99 Å
总原子数 total_atoms	1883
残基数 n_residues	235
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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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	58.3 Å
Rg (实空间) rg_real	17.96 Å
Rg 误差 (实空间) rg_real_error	0.34 Å
I(0) (实空间) i0_real	1.3670e+07
I(0) 误差 (实空间) i0_real_error	1.5470e+05
Rg (倒空间) rg_reciprocal	17.97 Å
I(0) (倒空间) i0_reciprocal	13670000.0000
解质量估计 total_estimate	0.8077
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	22.9 Å
偏度 Skewness skewness	0.197
峰度 Kurtosis kurtosis	-0.343
角度范围 angular_range	— – 0.4400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3705000.0000
实空间数据点数 n_real_points	75
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	ProAstacin
分子量 formula_weight	26437.4 kDa
EC 编号 ec_number	3.4.24.21
突变 mutation	I91L,E93A
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2252

SPIIPEAARALYYNDGMFEGDIKLRAGRQPARVGAAILGDEYLWSGGVIPYTFAGVSGADQSAILSGMQELEEKTCIRFVPRTTESDYVEIFTSGSGCWSYVGRISGAQQVSLQANGCVYHGTILHALMHAIGFYHEHTRMDRDNYVTINYQNVDPSMTSNFDIDTYSRYVGEDYQYYSIMHYGKYSFSIQWGVLETIVPLQNGIDLTDPYDKAHMLQTDANQINNLYTNECSLR

来源 Source

来源生物 organism	Astacus astacus
通用名 common_name	Broad-fingered crayfish
NCBI 分类编号 ncbi_taxonomy_id	6715
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

实体 4 Entity 4 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

实体 5 Entity 5 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	298

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7. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	3lq0A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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8. 引用文献 (1)

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晶胞边长 a length_a	55.910 Å
晶胞边长 b length_b	63.370 Å
晶胞边长 c length_c	69.190 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	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.450 Å
最低分辨率 resolution_low	41.920 Å
R 因子 r_factor	0.1522
R_work r_work	0.1517
R_free r_free	0.1805

fit	/app/data/saxs_computation/lq/3lq0/3lq0.fit
pddf	/app/data/pr_computation/lq/3lq0/3lq0.pr.out
profile	/app/data/saxs_computation/lq/3lq0/3lq0.dat

Zymogen structure of crayfish astacin metallopeptidase

1. 蛋白身份与相关结构 Protein Identity & Related Structures

ProAstacin

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction