SAXSdb — 1cfm

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

CYTOCHROME F

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 × 3 PDB 声明：trimeric（3）与蛋白拷贝数一致	链 A； UniProt 32–282 链 B； UniProt 32–282 链 C； UniProt 32–282	未记录	HEM PROTOPORPHYRIN IX CONTAINING FE × 3	X-RAY DIFFRACTION X-ray结晶条件：pH 6.5；pH 6.5	分辨率 2.00 Å R-free 0.271

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 1CFM	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
1E2V N153Q mutant of cytochrome f from Chlamydomonas reinhardtii 提交 2000-05-29	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 32–282（251 aa）	突变：YES	HEC HEME C × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 6.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.5, 25 MM CALCIUM ACETATE, 1 MM DTT AND 17-19% PEG 8000.	分辨率 1.85 Å R-free 0.219
1E2V N153Q mutant of cytochrome f from Chlamydomonas reinhardtii 提交 2000-05-29	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 32–282（251 aa）	突变：YES	HEC HEME C × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 6.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.5, 25 MM CALCIUM ACETATE, 1 MM DTT AND 17-19% PEG 8000.	分辨率 1.85 Å R-free 0.219
1E2V N153Q mutant of cytochrome f from Chlamydomonas reinhardtii 提交 2000-05-29	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 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 32–282（251 aa）	突变：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 6.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.5, 25 MM CALCIUM ACETATE, 1 MM DTT AND 17-19% PEG 8000.	分辨率 1.85 Å R-free 0.219
1E2W N168F mutant of cytochrome f from Chlamydomonas reinhardtii 提交 2000-05-30	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 32–282（251 aa）	突变：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, PH 7.5, 1 MM DTT, THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 200 MM AMMONIUM FORMATE, 14% GLYCEROL, 17% PEG-3350.	分辨率 1.60 Å R-free 0.226
1E2W N168F mutant of cytochrome f from Chlamydomonas reinhardtii 提交 2000-05-30	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 32–282（251 aa）	突变：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, PH 7.5, 1 MM DTT, THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 200 MM AMMONIUM FORMATE, 14% GLYCEROL, 17% PEG-3350.	分辨率 1.60 Å R-free 0.226
1E2Z Q158L mutant of cytochrome f from Chlamydomonas reinhardtii 提交 2000-05-30	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 32–282（251 aa）	突变：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 7.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 50 MM AMMONIUM FLUORIDE 5% GLYCEROL AND 19-21% PEG 3350.	分辨率 2.50 Å R-free 0.279
1E2Z Q158L mutant of cytochrome f from Chlamydomonas reinhardtii 提交 2000-05-30	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 32–282（251 aa）	突变：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 7.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 50 MM AMMONIUM FLUORIDE 5% GLYCEROL AND 19-21% PEG 3350.	分辨率 2.50 Å R-free 0.279
1E2Z Q158L mutant of cytochrome f from Chlamydomonas reinhardtii 提交 2000-05-30	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 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 32–282（251 aa）	突变：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 7.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 50 MM AMMONIUM FLUORIDE 5% GLYCEROL AND 19-21% PEG 3350.	分辨率 2.50 Å R-free 0.279
1EWH STRUCTURE OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII 提交 2000-04-25	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 32–282（251 aa）片段：N-TERMINAL SOLUBLE FRAGMENT	未记录	HEC HEME C × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, calcium acetate, MES, pH 6.5, VAPOR DIFFUSION, temperature 20K	分辨率 2.35 Å R-free 0.256
1EWH STRUCTURE OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII 提交 2000-04-25	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 32–282（251 aa）片段：N-TERMINAL SOLUBLE FRAGMENT	未记录	HEC HEME C × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, calcium acetate, MES, pH 6.5, VAPOR DIFFUSION, temperature 20K	分辨率 2.35 Å R-free 0.256
1EWH STRUCTURE OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII 提交 2000-04-25	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 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 32–282（251 aa）片段：N-TERMINAL SOLUBLE FRAGMENT	未记录	HEC HEME C × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, calcium acetate, MES, pH 6.5, VAPOR DIFFUSION, temperature 20K	分辨率 2.35 Å R-free 0.256
1Q90 Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii 提交 2003-08-22	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 × 18 PDB 声明：octadecameric	链 A 32–317（286 aa）片段：Residues 1-292	突变：6 His tag at C-terminus	HEC HEME C × 8 BCR BETA-CAROTENE × 2 LFA EICOSANE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 CLA CHLOROPHYLL A × 2 TDS 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；Reservoir: 25% PEG-MME 350, 40 millimolar TRIS HCL PH 8, 40 millimolar nacl, 0.2 millimolar laurylmaltoside, 30% glycerol. Drop: 1.3 microliter protein + 0.7 microliter reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 3.10 Å R-free 0.261
1Q90 Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii 提交 2003-08-22	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 × 36 PDB 声明：36-meric	链 A 32–317（286 aa）片段：Residues 1-292	突变：6 His tag at C-terminus	HEC HEME C × 16 BCR BETA-CAROTENE × 4 LFA EICOSANE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 4 CLA CHLOROPHYLL A × 4 TDS 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 8 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；Reservoir: 25% PEG-MME 350, 40 millimolar TRIS HCL PH 8, 40 millimolar nacl, 0.2 millimolar laurylmaltoside, 30% glycerol. Drop: 1.3 microliter protein + 0.7 microliter reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 277K	分辨率 3.10 Å R-free 0.261

共 5 个其他 PDB 条目、13 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	CYF_CHLRE
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–251； UniProt 32–282 作者链 B； PDB构建体 1–251； UniProt 32–282 作者链 C； PDB构建体 1–251； UniProt 32–282

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	1cfm
沉积日期 deposition_date	1998-09-18
结构标题 title	CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
关键词 keywords	CYTOCHROME F, PLASTOCYANIN, PROTON WIRE, HEME, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	35.59 Å
回转半径 Rg (电子) rg_electron	35.76 Å
零角强度 I(0) i0	102069000.00
分子量 molecular_weight	83312.0 kDa
排除体积 excluded_volume	105400 Å³
包络体积 envelope_volume	141810 Å³
水化壳体积 shell_volume	35638 Å³
包络直径 envelope_diameter	140.7 Å
壳层 Rg shell_rg	39.05 Å
包络 Rg envelope_rg	35.65 Å
形状 Rg shape_rg	35.74 Å
总 Rg total_rg	36.09 Å
总原子数 total_atoms	5877
残基数 n_residues	753
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	127.1 Å
Rg (实空间) rg_real	35.84 Å
Rg 误差 (实空间) rg_real_error	1.32 Å
I(0) (实空间) i0_real	1.0210e+08
I(0) 误差 (实空间) i0_real_error	1.6950e+06
Rg (倒空间) rg_reciprocal	35.69 Å
I(0) (倒空间) i0_reciprocal	102100000.0000
解质量估计 total_estimate	0.8429
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	34.7 Å
偏度 Skewness skewness	0.480
峰度 Kurtosis kurtosis	-0.313
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8455000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.751; Smooth: 0.887

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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 (3)

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7. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1cfma1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.6 — Cytochrome f, large domain
家族 Family family	b.2.6.1 — Cytochrome f, large domain

结构域编号 domain_id	d1cfma2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
家族 Family family	b.84.2.2 — Cytochrome f, small domain

结构域编号 domain_id	d1cfmb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.6 — Cytochrome f, large domain
家族 Family family	b.2.6.1 — Cytochrome f, large domain

结构域编号 domain_id	d1cfmb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
家族 Family family	b.84.2.2 — Cytochrome f, small domain

结构域编号 domain_id	d1cfmc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.6 — Cytochrome f, large domain
家族 Family family	b.2.6.1 — Cytochrome f, large domain

结构域编号 domain_id	d1cfmc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
家族 Family family	b.84.2.2 — Cytochrome f, small domain

CATH v4.4 (6 domains)

结构域编号 domain_id	1cfmA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	830 — Cytochrome f large domain

结构域编号 domain_id	1cfmA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	1cfmB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	830 — Cytochrome f large domain

结构域编号 domain_id	1cfmB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	1cfmC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	830 — Cytochrome f large domain

结构域编号 domain_id	1cfmC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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8. 引用文献 (1)

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晶胞边长 a length_a	75.624 Å
晶胞边长 b length_b	94.943 Å
晶胞边长 c length_c	119.920 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	12

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	2.000 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2710

描述 description	CYTOCHROME F
分子量 formula_weight	27182.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	6878

CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII

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

CYTOCHROME F

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

6. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 non-polymer

实体 3 Entity 3 water

7. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1001

fit	/app/data/saxs_computation/cf/1cfm/1cfm.fit
pddf	/app/data/pr_computation/cf/1cfm/1cfm.pr.out
profile	/app/data/saxs_computation/cf/1cfm/1cfm.dat