1d4c

CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1

Method: X-RAY DIFFRACTION D_max: 173.8 Å Quality: GOOD

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

FLAVOCYTOCHROME C FUMARATE REDUCTASE

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	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 25–596	未记录	HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；ammonium sulfate with added PEG 400, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	分辨率 2.90 Å R-free 0.300
2	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 B； UniProt 25–596	未记录	HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；ammonium sulfate with added PEG 400, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	分辨率 2.90 Å R-free 0.300
3	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 C； UniProt 25–596	未记录	HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；ammonium sulfate with added PEG 400, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	分辨率 2.90 Å R-free 0.300
4	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 D； UniProt 25–596	未记录	HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；ammonium sulfate with added PEG 400, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	分辨率 2.90 Å R-free 0.300

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 1D4C	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
1D4D CRYSTAL STRUCTURE OF THE SUCCINATE COMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1 提交 1999-10-03	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 25–596（572 aa）	未记录	HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；ammonium sulfate with added ethanol and succinate, bicine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	分辨率 2.50 Å R-free 0.305
1D4E CRYSTAL STRUCTURE OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1 COMPLEXED WITH FUMARATE 提交 1999-10-03	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 25–596（572 aa）	未记录	HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FUM FUMARIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；ammonium sulfate with ethanol and fumarate added, bicine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	分辨率 2.80 Å R-free 0.311

共 2 个其他 PDB 条目、2 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	FRDA_SHEON
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–572； UniProt 25–596 作者链 B； PDB构建体 1–572； UniProt 25–596 作者链 C； PDB构建体 1–572； UniProt 25–596 作者链 D； PDB构建体 1–572； UniProt 25–596

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	1d4c
沉积日期 deposition_date	1999-10-03
结构标题 title	CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1
关键词 keywords	TETRAHEME FLAVOCYTOCHROME C, 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	54.37 Å
回转半径 Rg (电子) rg_electron	54.13 Å
零角强度 I(0) i0	925669000.00
分子量 molecular_weight	247140.0 kDa
排除体积 excluded_volume	305740 Å³
包络体积 envelope_volume	448620 Å³
水化壳体积 shell_volume	68168 Å³
包络直径 envelope_diameter	173.8 Å
壳层 Rg shell_rg	60.02 Å
包络 Rg envelope_rg	51.34 Å
形状 Rg shape_rg	54.13 Å
总 Rg total_rg	54.28 Å
总原子数 total_atoms	17344
残基数 n_residues	2274
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	173.8 Å
Rg (实空间) rg_real	54.27 Å
Rg 误差 (实空间) rg_real_error	1.75 Å
I(0) (实空间) i0_real	9.2570e+08
I(0) 误差 (实空间) i0_real_error	2.0340e+07
Rg (倒空间) rg_reciprocal	54.42 Å
I(0) (倒空间) i0_reciprocal	925800000.0000
解质量估计 total_estimate	0.8622
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	77.9 Å
偏度 Skewness skewness	0.041
峰度 Kurtosis kurtosis	-0.786
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	39330000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.690

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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	FLAVOCYTOCHROME C FUMARATE REDUCTASE
分子量 formula_weight	59974.7 kDa
EC 编号 ec_number	1.3.99.1
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	17470

AAPEVLADFHGEMGGCDSCHVSDKGGVTNDNLTHENGQCVSCHGDLKELAAAAPKDKVSPHKSHLIGEIACTSCHKGHEKSVAYCDACHSFGFDMPFGGKWERKFVPVDADKAAQDKAIAAGVKETTDVVIIGSGGAGLAAAVSARDAGAKVILLEKEPIPGGNTKLAAGGMNAAETKPQAKLGIEDKKQIMIDDTMKGGRNINDPELVKVLANNSSDSIDWLTSMGADMTDVGRMGGASVNRSHRPTGGAGVGAHVAQVLWDNAVKRGTDIRLNSRVVRILEDASGKVTGVLVKGEYTGYYVIKADAVVIAAGGFAKNNERVSKYDPKLKGFKATNHPGATGDGLDVALQAGAATRDLEYIQAHPTYSPAGGVMITEAVRGNGAIVVNREGNRFMNEITTRDKASAAILQQKGESAYLVFDDSIRKSLKAIEGYVHLNIVKEGKTIEELAKQIDVPAAELAKTVTAYNGFVKSGKDAQFERPDLPRELVVAPFYALEIAPAVHHTMGGLVIDTKAEVKSEKTGKPITGLYAAGEVTGGVHGANRLGGNAISDIVTYGRIAGASAAKFAKDN

实体 2 Entity 2 non-polymer

描述 description	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

实体 3 Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 4 Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	126

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7. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1d4ca1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.138 — Multiheme cytochromes
超家族 Superfamily superfamily	a.138.1 — Multiheme cytochromes
家族 Family family	a.138.1.3 — Di-heme elbow motif

结构域编号 domain_id	d1d4ca2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

结构域编号 domain_id	d1d4ca3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
超家族 Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
家族 Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

结构域编号 domain_id	d1d4cb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.138 — Multiheme cytochromes
超家族 Superfamily superfamily	a.138.1 — Multiheme cytochromes
家族 Family family	a.138.1.3 — Di-heme elbow motif

结构域编号 domain_id	d1d4cb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

结构域编号 domain_id	d1d4cb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
超家族 Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
家族 Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

结构域编号 domain_id	d1d4cc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.138 — Multiheme cytochromes
超家族 Superfamily superfamily	a.138.1 — Multiheme cytochromes
家族 Family family	a.138.1.3 — Di-heme elbow motif

结构域编号 domain_id	d1d4cc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

结构域编号 domain_id	d1d4cc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
超家族 Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
家族 Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

结构域编号 domain_id	d1d4cd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.138 — Multiheme cytochromes
超家族 Superfamily superfamily	a.138.1 — Multiheme cytochromes
家族 Family family	a.138.1.3 — Di-heme elbow motif

结构域编号 domain_id	d1d4cd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

结构域编号 domain_id	d1d4cd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
超家族 Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
家族 Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

CATH v4.4 (12 domains)

结构域编号 domain_id	1d4cA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

结构域编号 domain_id	1d4cA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1d4cA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

结构域编号 domain_id	1d4cB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

结构域编号 domain_id	1d4cB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1d4cB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

结构域编号 domain_id	1d4cC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

结构域编号 domain_id	1d4cC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1d4cC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

结构域编号 domain_id	1d4cD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

结构域编号 domain_id	1d4cD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1d4cD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

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8. 引用文献 (1)

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晶胞边长 a length_a	109.690 Å
晶胞边长 b length_b	216.360 Å
晶胞边长 c length_c	112.040 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 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	—
R_work r_work	0.2100
R_free r_free	0.3000

fit	/app/data/saxs_computation/d4/1d4c/1d4c.fit
pddf	/app/data/pr_computation/d4/1d4c/1d4c.pr.out
profile	/app/data/saxs_computation/d4/1d4c/1d4c.dat