1b25

FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS

Method: X-RAY DIFFRACTION D_max: 139.4 Å Quality: GOOD

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

PROTEIN (FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE)

物种未注明

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	蛋白同源多聚体同源多聚体蛋白 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链未唯一映射； UniProt —–— 链 A； UniProt 1–619	片段：DOMAIN 1: 1-208, DOMAIN 2: 209-406, DOMAIN 3: 407-619	SF4 IRON/SULFUR CLUSTER × 4 PTT Oxo-tungstopterin cofactor × 4 MG MAGNESIUM ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件：pH 5.6；pH 5.6	分辨率 1.85 Å R-free 0.220

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 1B25	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
1B4N FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS, COMPLEXED WITH GLUTARATE 提交 1998-12-24	构建体不同突变/修饰不同配体/离子不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 1–619（619 aa）片段：DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619 链 B 1–619（619 aa）片段：DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619 链 C 1–619（619 aa）片段：DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619 链 D 1–619（619 aa）片段：DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619	未记录	CA CALCIUM ION × 4 SF4 IRON/SULFUR CLUSTER × 4 GUA GLUTARIC ACID × 4 PTE TUNGSTOPTERIN COFACTOR × 4	X-RAY DIFFRACTION X-ray结晶条件 pH 5.6；pH 5.6	分辨率 2.40 Å R-free 0.244

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	O93738_PYRFU
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–619； UniProt 1–619

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

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1b25
沉积日期 deposition_date	1998-12-04
结构标题 title	FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS
关键词 keywords	MOCO, TUNGSTOENZYME, TUNGSTEN CONTAINING PROTEIN, HYPERTHERMOPHILE, OXIDOREDUCTASE; OXIDOREDUCTASE
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	46.11 Å
回转半径 Rg (电子) rg_electron	45.97 Å
零角强度 I(0) i0	1096230000.00
分子量 molecular_weight	277190.0 kDa
排除体积 excluded_volume	346640 Å³
包络体积 envelope_volume	428230 Å³
水化壳体积 shell_volume	73587 Å³
包络直径 envelope_diameter	145.0 Å
壳层 Rg shell_rg	54.89 Å
包络 Rg envelope_rg	44.95 Å
形状 Rg shape_rg	46.07 Å
总 Rg total_rg	45.89 Å
总原子数 total_atoms	19384
残基数 n_residues	2444
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	139.4 Å
Rg (实空间) rg_real	45.89 Å
Rg 误差 (实空间) rg_real_error	1.04 Å
I(0) (实空间) i0_real	1.0960e+09
I(0) 误差 (实空间) i0_real_error	1.9620e+07
Rg (倒空间) rg_reciprocal	46.11 Å
I(0) (倒空间) i0_reciprocal	1097000000.0000
解质量估计 total_estimate	0.8696
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	69.7 Å
偏度 Skewness skewness	0.025
峰度 Kurtosis kurtosis	-0.722
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	384900000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.532

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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 (6)

实体 1 Entity 1 polymer

描述 description	PROTEIN (FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE)
分子量 formula_weight	68860.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	20733

MYGWWGRILRVNLTTGEVKVQEYPEEVAKKFIGGRGLAAWILWNEARGVEPLSPENKLIFAAGPFNGLPTPSGGKLVVAAKSPLTGGYGDGNLGTMASVHLRRAGYDALVVEGKAKKPVYIYIEDDNVSILSAEGLWGKTTFETERELKEIHGKNVGVLTIGPAGENLVKYAVVISQEGRAAGRPGMGAVMGSKKLKAVVIRGTKEIPVADKEELKKLSQEAYNEILNSPGYPFWKRQGTMAAVEWCNTNYALPTRNFSDGYFEFARSIDGYTMEGMKVQQRGCPYCNMPCGNVVLDAEGQESELDYENVALLGSNLGIGKLNEVSVLNRIADEMGMDTISLGVSIAHVMEAVERGILKEGPTFGDFKGAKQLALDIAYRKGELGNLAAEGVKAMAEKLGTHDFAMHVKGLEVSGYNCYIYPAMALAYGTSAIGAHHKEAWVIAWEIGTAPIEGEKAEKVEYKISYDPIKAQKVVELQRLRGGLFEMLTACRLPWVEVGLSLDYYPKLLKAITGVTYTWDDLYKAADRVYSLIRAYWVREFNGKWDRKMDYPPKRWFTEGLKSGPHKGEHLDEKKYDELLSEYYRIRGWDERGIPKKETLKELDLDFVIPELEKVTNLE

实体 2 Entity 2 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 3 Entity 3 non-polymer

描述 description	Oxo-tungstopterin cofactor
分子量 formula_weight	987.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 4 Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

实体 5 Entity 5 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

实体 6 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	1349

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7. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1b25a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.110 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
超家族 Superfamily superfamily	a.110.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
家族 Family family	a.110.1.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains

结构域编号 domain_id	d1b25a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.152 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
超家族 Superfamily superfamily	d.152.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
家族 Family family	d.152.1.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

结构域编号 domain_id	d1b25b1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.110 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
超家族 Superfamily superfamily	a.110.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
家族 Family family	a.110.1.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains

结构域编号 domain_id	d1b25b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.152 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
超家族 Superfamily superfamily	d.152.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
家族 Family family	d.152.1.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

结构域编号 domain_id	d1b25c1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.110 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
超家族 Superfamily superfamily	a.110.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
家族 Family family	a.110.1.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains

结构域编号 domain_id	d1b25c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.152 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
超家族 Superfamily superfamily	d.152.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
家族 Family family	d.152.1.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

结构域编号 domain_id	d1b25d1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.110 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
超家族 Superfamily superfamily	a.110.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
家族 Family family	a.110.1.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains

结构域编号 domain_id	d1b25d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.152 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
超家族 Superfamily superfamily	d.152.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
家族 Family family	d.152.1.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

CATH v4.4 (12 domains)

结构域编号 domain_id	1b25A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	9 — Aldehyde Ferredoxin Oxidoreductase; A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

结构域编号 domain_id	1b25A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	569 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2

结构域编号 domain_id	1b25A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	599 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3

结构域编号 domain_id	1b25B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	9 — Aldehyde Ferredoxin Oxidoreductase; A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

结构域编号 domain_id	1b25B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	569 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2

结构域编号 domain_id	1b25B03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	599 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3

结构域编号 domain_id	1b25C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	9 — Aldehyde Ferredoxin Oxidoreductase; A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

结构域编号 domain_id	1b25C02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	569 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2

结构域编号 domain_id	1b25C03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	599 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3

结构域编号 domain_id	1b25D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	9 — Aldehyde Ferredoxin Oxidoreductase; A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

结构域编号 domain_id	1b25D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	569 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2

结构域编号 domain_id	1b25D03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	599 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3

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8. 引用文献 (2)

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晶胞边长 a length_a	100.340 Å
晶胞边长 b length_b	170.850 Å
晶胞边长 c length_c	180.640 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	16

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	1.850 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1740
R_work r_work	0.1740
R_free r_free	0.2200

fit	/app/data/saxs_computation/b2/1b25/1b25.fit
pddf	/app/data/pr_computation/b2/1b25/1b25.pr.out
profile	/app/data/saxs_computation/b2/1b25/1b25.dat