8thm

Beta carbonic anhydrase from the carboxysome of Cyanobium PCC 7001

Method: X-RAY DIFFRACTION D_max: 148.7 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	8thm
沉积日期 deposition_date	2023-07-17
结构标题 title	Beta carbonic anhydrase from the carboxysome of Cyanobium PCC 7001
关键词 keywords	beta-carbonic anhydrase, carboxysome, cyanobacteria, RuBP activated, LYASE, PHOTOSYNTHESIS; PHOTOSYNTHESIS
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	48.40 Å
回转半径 Rg (电子) rg_electron	47.47 Å
零角强度 I(0) i0	1515240000.00
分子量 molecular_weight	311910.0 kDa
排除体积 excluded_volume	384670 Å³
包络体积 envelope_volume	517690 Å³
水化壳体积 shell_volume	87861 Å³
包络直径 envelope_diameter	158.1 Å
壳层 Rg shell_rg	55.22 Å
包络 Rg envelope_rg	45.84 Å
形状 Rg shape_rg	47.46 Å
总 Rg total_rg	47.72 Å
总原子数 total_atoms	22004
残基数 n_residues	2769
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	148.7 Å
Rg (实空间) rg_real	47.97 Å
Rg 误差 (实空间) rg_real_error	0.96 Å
I(0) (实空间) i0_real	1.5150e+09
I(0) 误差 (实空间) i0_real_error	2.5260e+07
Rg (倒空间) rg_reciprocal	48.40 Å
I(0) (倒空间) i0_reciprocal	1516000000.0000
解质量估计 total_estimate	0.8713
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	67.6 Å
偏度 Skewness skewness	-0.044
峰度 Kurtosis kurtosis	-0.517
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	454800000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.870

▶

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

▶

5. 实体与聚合体信息 (9)

Entity 1 polymer

描述 description	Carboxysome shell carbonic anhydrase
分子量 formula_weight	51308.6 kDa
EC 编号 ec_number	4.2.1.1
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	23086

SMHPLTDASANDALHAYDTAVKLAFDRIVPVLKRLSALQHEDDFVGRAQAIALEELGFPLPEPILDTAWVSQLDMRTLYAWCVFETYEQTSEAFFRDDPLQGQPGSPSAEAFDRFLLDCGFHLLDITPCADGRLAHAIGFGLRLPFSSVRRRPHAGALFDVENTVNRWVKTEHRRYREAQPNPAHADTRYLKVALYHFSSLDPQHEGCAAHGSDDALAASCGLSRLKDFQQAVENSFCCGASVDLLLMGIDTDTDAIRVHVPGMDGSTRLDRWLDARDVYDATLGLPPDQARQRVSALVQEAAASVPDPGMVTLVARLFEHNISQIDYVRQFHGGAYDDAGHAERFIGVGIGFKEIHLRNLTYFAYMDTVEEGAADLDVGVKIFKGLNVSRGLPVPVVVRFDYHGQVPGARDRAVRHCQRVQTAIESRYPELFQQGLLHALLTVRDQDRHTPAEAVGSTIVF

来源 Source

来源生物 organism	Cyanobium sp. PCC 7001
NCBI 分类编号 ncbi_taxonomy_id	180281
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	8

Entity 3 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	3

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	18

Entity 5 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 6 non-polymer

描述 description	RIBULOSE-1,5-DIPHOSPHATE
分子量 formula_weight	310.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 7 non-polymer

描述 description	CARBON DIOXIDE
分子量 formula_weight	44.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 non-polymer

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

Entity 9 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	773

▼

6. 折叠分类 (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

结构域编号 domain_id	8thmA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	1310 — Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain

结构域编号 domain_id	8thmA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	140 — Carboxysome Shell Carbonic Anhydrase, C-terminal domain

结构域编号 domain_id	8thmB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	1310 — Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain

结构域编号 domain_id	8thmB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	140 — Carboxysome Shell Carbonic Anhydrase, C-terminal domain

结构域编号 domain_id	8thmC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	1310 — Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain

结构域编号 domain_id	8thmC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	140 — Carboxysome Shell Carbonic Anhydrase, C-terminal domain

结构域编号 domain_id	8thmD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	1310 — Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain

结构域编号 domain_id	8thmD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	140 — Carboxysome Shell Carbonic Anhydrase, C-terminal domain

结构域编号 domain_id	8thmE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	1310 — Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain

结构域编号 domain_id	8thmE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	140 — Carboxysome Shell Carbonic Anhydrase, C-terminal domain

结构域编号 domain_id	8thmF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	140 — Carboxysome Shell Carbonic Anhydrase, C-terminal domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	104.314 Å
晶胞边长 b length_b	181.848 Å
晶胞边长 c length_c	190.057 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	24

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	2.300 Å
最低分辨率 resolution_low	47.510 Å
R 因子 r_factor	0.1958
R_work r_work	0.1930
R_free r_free	0.2475

fit	/app/data/saxs_computation/th/8thm/8thm.fit
pddf	/app/data/pr_computation/th/8thm/8thm.pr.out
profile	/app/data/saxs_computation/th/8thm/8thm.dat