1oao

NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase

Method: X-RAY DIFFRACTION D_max: 192.3 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1oao
沉积日期 deposition_date	2003-01-20
结构标题 title	NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase
关键词 keywords	OXIDOREDUCTASE-TRANSFERASE COMPLEX, ELECTRON TRANSFER, OXIDOREDUCTASE, ACETYL-COA FORMATION, WOOD/LJUNGDAHL PATHWAY, NICKEL; OXIDOREDUCTASE/TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	52.34 Å
回转半径 Rg (电子) rg_electron	53.34 Å
零角强度 I(0) i0	1497690000.00
分子量 molecular_weight	315670.0 kDa
排除体积 excluded_volume	392200 Å³
包络体积 envelope_volume	498920 Å³
水化壳体积 shell_volume	83479 Å³
包络直径 envelope_diameter	203.0 Å
壳层 Rg shell_rg	50.16 Å
包络 Rg envelope_rg	54.65 Å
形状 Rg shape_rg	53.42 Å
总 Rg total_rg	52.96 Å
总原子数 total_atoms	21955
残基数 n_residues	2803
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	192.3 Å
Rg (实空间) rg_real	53.00 Å
Rg 误差 (实空间) rg_real_error	3.32 Å
I(0) (实空间) i0_real	1.4980e+09
I(0) 误差 (实空间) i0_real_error	3.7580e+07
Rg (倒空间) rg_reciprocal	51.81 Å
I(0) (倒空间) i0_reciprocal	1495000000.0000
解质量估计 total_estimate	0.7605
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	44.9 Å
偏度 Skewness skewness	0.798
峰度 Kurtosis kurtosis	0.354
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	257800000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.543; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.359

▶

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

▶

5. 实体与聚合体信息 (14)

Entity 1 polymer

描述 description	CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT BETA
分子量 formula_weight	73006.9 kDa
EC 编号 ec_number	1.2.99.2, 1.2.7.4
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	23346

MPRFRDLSHNCRPSEAPRVMEPKNRDRTVDPAVLEMLVKSKDDKVITAFDRFVAQQPQCKIGYEGICCRFCMAGPCRIKATDGPGSRGICGASAWTIVARNVGLMILTGAAAHCEHGNHIAHALVEMAEGKAPDYSVKDEAKLKEVCRRVGIEVEGKSVLELAQEVGEKALEDFRRLKGEGEATWLMTTINEGRKEKFRTHNVVPFGIHASISELVNQAHMGMDNDPVNLVFSAIRVALADYTGEHIATDFSDILFGTPQPVVSEANMGVLDPDQVNFVLHGHNPLLSEIIVQAAREMEGEAKAAGAKGINLVGICCTGNEVLMRQGIPLVTSFASQELAICTGAIDAMCVDVQCIMPSISAVAECYHTRIITTADNAKIPGAYHIDYQTATAIESAKTAIRMAIEAFKERKESNRPVYIPQIKNRVVAGWSLEALTKLLATQNAQNPIRVLNQAILDGELAGVALICGCNNLKGFQDNSHLTVMKELLKNNVFVVATGCSAQAAGKLGLLDPANVETYCGDGLKGFLKRLGEGANIEIGLPPVFHMGSCVDNSRAVDLLMAMANDLGVDTPKVPFVASAPEAMSGKAAAIGTWWVSLGVPTHVGTMPPVEGSDLIYSILTQIASDVYGGYFIFEMDPQVAARKILDALEYRTWKLGVHKEVAERYETKLCQGY

Entity 2 polymer

描述 description	CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ALPHA
分子量 formula_weight	81816.9 kDa
EC 编号 ec_number	2.3.1.169
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D

MTDFDKIFEGAIPEGKEPVALFREVYHGAITATSYAEILLNQAIRTYGPDHPVGYPDTAYYLPVIRCFSGEEVKKLGDLPPILNRKRAQVSPVLNFENARLAGEATWYAAEIIEALRYLKYKPDEPLLPPPWTGFIGDPVVRRFGIKMVDWTIPGEAIILGRAKDSKALAKIVKELMGMGFMLFICDEAVEQLLEENVKLGIDYIAYPLGNFTQIVHAANYALRAGMMFGGVTPGAREEQRDYQRRRIRAFVLYLGEHDMVKTAAAFGAIFTGFPVITDQPLPEDKQIPDWFFSVEDYDKIVQIAMETRGIKLTKIKLDLPINFGPAFEGESIRKGDMYVEMGGNRTPAFELVRTVSESEITDGKIEVIGPDIDQIPEGSKLPLGILVDIYGRKMQADFEGVLERRIHDFINYGEGLWHTGQRNINWLRVSKDAVAKGFRFKNYGEILVAKMKEEFPAIVDRVQVTIFTDEAKVKEYMEVAREKYKERDDRMRGLTDETVDTFYSCVLCQSFAPNHVCIVTPERVGLCGAVSWLDAKASYEINHAGPNQPIPKEGEIDPIKGIWKSVNDYLYTASNRNLEQVCLYTLMENPMTSCGCFEAIMAILPECNGIMITTRDHAGMTPSGMTFSTLAGMIGGGTQTPGFMGIGRTYIVSKKFISADGGIARIVWMPKSLKDFLHDEFVRRSVEEGLGEDFIDKIADETIGTTVDEILPYLEEKGHPALTMDPIM

Entity 3 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	5

Entity 4 non-polymer

描述 description	FE(4)-NI(1)-S(4) CLUSTER
分子量 formula_weight	410.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	FORMYL GROUP
分子量 formula_weight	30.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	31

Entity 7 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 8 non-polymer

描述 description	FE (II) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	BICARBONATE ION
分子量 formula_weight	61.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 non-polymer

描述 description	NICKEL (II) ION
分子量 formula_weight	58.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 12 non-polymer

描述 description	SULFUR OXIDE
分子量 formula_weight	48.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 13 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 14 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	1271

▼

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1oaoa_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.26 — Prismane protein-like
超家族 Superfamily superfamily	e.26.1 — Prismane protein-like
家族 Family family	e.26.1.2 — Carbon monoxide dehydrogenase

结构域编号 domain_id	d1oaob_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.26 — Prismane protein-like
超家族 Superfamily superfamily	e.26.1 — Prismane protein-like
家族 Family family	e.26.1.2 — Carbon monoxide dehydrogenase

结构域编号 domain_id	d1oaoc_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.26 — Prismane protein-like
超家族 Superfamily superfamily	e.26.1 — Prismane protein-like
家族 Family family	e.26.1.3 — Acetyl-CoA synthase

结构域编号 domain_id	d1oaod_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.26 — Prismane protein-like
超家族 Superfamily superfamily	e.26.1 — Prismane protein-like
家族 Family family	e.26.1.3 — Acetyl-CoA synthase

CATH v4.4 (16 domains)

结构域编号 domain_id	1oaoA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2030 —

结构域编号 domain_id	1oaoA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2030 —

结构域编号 domain_id	1oaoA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1oaoB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2030 —

结构域编号 domain_id	1oaoB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2030 —

结构域编号 domain_id	1oaoB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1oaoC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1

结构域编号 domain_id	1oaoC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2030 —

结构域编号 domain_id	1oaoC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3

结构域编号 domain_id	1oaoC04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	970 — Ribonuclease HI; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4

结构域编号 domain_id	1oaoC05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
同源超家族 H-superfamily homologous superfamily	10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5

结构域编号 domain_id	1oaoD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1

结构域编号 domain_id	1oaoD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2030 —

结构域编号 domain_id	1oaoD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3

结构域编号 domain_id	1oaoD04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	970 — Ribonuclease HI; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4

结构域编号 domain_id	1oaoD05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
同源超家族 H-superfamily homologous superfamily	10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	244.570 Å
晶胞边长 b length_b	81.890 Å
晶胞边长 c length_c	167.220 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.19 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.1490
R_work r_work	0.1470
R_free r_free	0.1790

fit	/app/data/saxs_computation/oa/1oao/1oao.fit
pddf	/app/data/pr_computation/oa/1oao/1oao.pr.out
profile	/app/data/saxs_computation/oa/1oao/1oao.dat

NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (14)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

CATH v4.4 (16 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)