1fdd

AZOTOBACTER VINELANDII FERREDOXIN I: ASPARTATE 15 FACILITATES PROTON TRANSFER TO THE REDUCED [3FE-4S] CLUSTER

Method: X-RAY DIFFRACTION D_max: 43.0 Å Quality: GOOD

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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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fdd
沉积日期 deposition_date	1993-01-17
结构标题 title	AZOTOBACTER VINELANDII FERREDOXIN I: ASPARTATE 15 FACILITATES PROTON TRANSFER TO THE REDUCED [3FE-4S] CLUSTER
关键词 keywords	ELECTRON TRANSPORT(IRON-SULFUR); ELECTRON TRANSPORT(IRON-SULFUR)
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	13.45 Å
回转半径 Rg (电子) rg_electron	12.34 Å
零角强度 I(0) i0	3731260.00
分子量 molecular_weight	12680.0 kDa
排除体积 excluded_volume	15276 Å³
包络体积 envelope_volume	16008 Å³
水化壳体积 shell_volume	10864 Å³
包络直径 envelope_diameter	40.7 Å
壳层 Rg shell_rg	18.37 Å
包络 Rg envelope_rg	12.74 Å
形状 Rg shape_rg	12.45 Å
总 Rg total_rg	13.27 Å
总原子数 total_atoms	856
残基数 n_residues	106
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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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	43.0 Å
Rg (实空间) rg_real	13.36 Å
Rg 误差 (实空间) rg_real_error	0.20 Å
I(0) (实空间) i0_real	3.7310e+06
I(0) 误差 (实空间) i0_real_error	3.8710e+04
Rg (倒空间) rg_reciprocal	13.37 Å
I(0) (倒空间) i0_reciprocal	3731000.0000
解质量估计 total_estimate	0.8910
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	16.3 Å
偏度 Skewness skewness	0.116
峰度 Kurtosis kurtosis	-0.404
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	490100.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.987

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	FERREDOXIN
分子量 formula_weight	12058.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	879

AFVVTDNCIKCKYTNCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER

来源 Source

来源生物 organism	Azotobacter vinelandii
NCBI 分类编号 ncbi_taxonomy_id	354

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	1

Entity 3 non-polymer

描述 description	FE3-S4 CLUSTER
分子量 formula_weight	295.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	23

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1fdda_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
家族 Family family	d.58.1.2 — 7-Fe ferredoxin

CATH v4.4 (1 domains)

结构域编号 domain_id	1fddA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (13)

Azotobacter vinelandii ferredoxin I. Aspartate 15 facilitates proton transfer to the reduced [3Fe-4S] cluster.

J.Biol.Chem. (1993)

PMID: 8245026 PRIMARY

Crystallographic Analysis of Two Site-Directed Mutants of Azotobacter Vinelandii Ferredoxin

J.Biol.Chem. (1991)

Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement

Proc.Natl.Acad.Sci.USA (1990)

Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution

J.Mol.Biol. (1989)

7-Iron Ferredoxin Revisited

J.Biol.Chem. (1988)

(4Fe-4S)-Cluster-Depleted Azotobacter Vinelandii Ferredoxin I. A New 3Fe Iron-Sulfur Protein

Proc.Natl.Acad.Sci.USA (1985)

Structure of Azotobacter Vinelandii 7Fe Ferredoxin. Amino Acid Sequence and Electron Density Maps of Residues

J.Biol.Chem. (1983)

Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Angstroms Resolution

J.Mol.Biol. (1982)

Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii

J.Biol.Chem. (1981)

Iron-Sulfur Clusters in Azotobacter Ferredoxin at 2.5 Angstroms Resolution

J.Biol.Chem. (1980)

Structure of the Iron-Sulfur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution

Am.Cryst.Assoc.,Abstr.Papers (Winter Meeting) (1979)

Two Crystal Forms of Azotobacter Ferredoxin

J.Biol.Chem. (1979)

Structure of the Iron-Sulphur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution

Nature (1979)

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晶胞边长 a length_a	55.600 Å
晶胞边长 b length_b	55.600 Å
晶胞边长 c length_c	95.900 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	8

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	—

fit	/app/data/saxs_computation/fd/1fdd/1fdd.fit
pddf	/app/data/pr_computation/fd/1fdd/1fdd.pr.out
profile	/app/data/saxs_computation/fd/1fdd/1fdd.dat