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6saz

Cleaved human fetuin-b in complex with crayfish astacin

Method: X-RAY DIFFRACTION Dmax: 126.7 Å Quality: GOOD
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Astacin

物种未注明

UniProt P07584

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 其他组合 异源复合物 蛋白 × 2 其他聚合物 2 PDB 声明：dimeric（2） 与蛋白拷贝数一致 链 A； UniProt 50–251 未记录 Fetuin-B × 1 （Q9UGM5） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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
2 其他组合 异源复合物 蛋白 × 2 其他聚合物 1 PDB 声明：dimeric（2） 与蛋白拷贝数一致 链 C； UniProt 50–251 未记录 Fetuin-B × 1 （Q9UGM5） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 6SAZ 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 聚集状态不同 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 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 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 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 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 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 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 聚集状态不同 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
3LQ0 Zymogen structure of crayfish astacin metallopeptidase 提交 2010-02-08 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 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric
链 A 16–250（235 aa）
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
6HT9 Mouse fetuin-B in complex with crayfish astacin 提交 2018-10-03 构建体不同 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 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

共 10 个其他 PDB 条目、11 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_ASTAS
Isoform —
PDB实体 1
链与序列区间 作者链 A； PDB构建体 1–202； UniProt 50–251 作者链 C； PDB构建体 1–202； UniProt 50–251

Fetuin-B

Homo sapiens

UniProt Q9UGM5

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 其他组合 异源复合物 蛋白 × 2 其他聚合物 2 PDB 声明：dimeric（2） 与蛋白拷贝数一致 链 B； UniProt 1–382 未记录 Astacin × 1 （P07584） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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
2 其他组合 异源复合物 蛋白 × 2 其他聚合物 1 PDB 声明：dimeric（2） 与蛋白拷贝数一致 链 D； UniProt 1–382 未记录 Astacin × 1 （P07584） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 6SAZ 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
7UAI Meprin alpha helix in complex with fetuin-B 提交 2022-03-13 构建体不同 突变/修饰不同 聚集状态不同 配体/离子不同 实验方法不同 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 × 6 PDB 声明：hexameric
链 A 1–382（382 aa）
链 H 1–382（382 aa）
未记录 CA CALCIUM ION × 8 ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM缓冲液 pH 7.4
cryo-EM玻璃化条件 冷冻剂 ETHANE；3 s blot, -3 force
分辨率 2.80 Å

共 1 个其他 PDB 条目、1 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 FETUB_HUMAN
Isoform —
PDB实体 2
链与序列区间 作者链 B； PDB构建体 1–382； UniProt 1–382 作者链 D； PDB构建体 1–382； UniProt 1–382

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。

SAXS 散射曲线 SAXS Profile

SAXS profile for 6saz

P(r) 距离分布 P(r) Distribution

P(r) distribution for 6saz
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id6saz
沉积日期 deposition_date2019-07-18
结构标题 titleCleaved human fetuin-b in complex with crayfish astacin
关键词 keywordsmammalian fertilization, sperm-egg fusion, polyspermy, metallopeptidase, protein inhibitor, limited proteolysis, HYDROLASE; HYDROLASE
实验方法 methodX-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_guinier37.04 Å
回转半径 Rg (电子) rg_electron36.77 Å
零角强度 I(0) i0159457000.00
分子量 molecular_weight99342.0 kDa
排除体积 excluded_volume123130 ų
包络体积 envelope_volume168330 ų
水化壳体积 shell_volume39286 ų
包络直径 envelope_diameter133.0 Å
壳层 Rg shell_rg41.00 Å
包络 Rg envelope_rg37.25 Å
形状 Rg shape_rg36.73 Å
总 Rg total_rg37.21 Å
总原子数 total_atoms6974
残基数 n_residues864
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 Å−1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3
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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax126.7 Å
Rg (实空间) rg_real37.20 Å
Rg 误差 (实空间) rg_real_error0.96 Å
I(0) (实空间) i0_real1.5950e+08
I(0) 误差 (实空间) i0_real_error2.5510e+06
Rg (倒空间) rg_reciprocal37.11 Å
I(0) (倒空间) i0_reciprocal159400000.0000
解质量估计 total_estimate0.8661
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary44.2 Å
偏度 Skewness skewness0.379
峰度 Kurtosis kurtosis-0.421
角度范围 angular_range— – 0.2150 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha17370000.0000
实空间数据点数 n_real_points44
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.826; Smooth: 0.830
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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 (7)

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7. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_idd6saza_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.92 — Zincin-like
超家族 Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family familyd.92.1.8 — Astacin
结构域编号 domain_idd6sazc_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.92 — Zincin-like
超家族 Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family familyd.92.1.8 — Astacin

CATH v4.4 (2 domains)

结构域编号 domain_id6sazA00
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
结构域编号 domain_id6sazC00
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
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8. 引用文献 (2)

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9. 文件与曲线 (10)