2glj

crystal structure of aminopeptidase I from Clostridium acetobutylicum

Method: X-RAY DIFFRACTION D_max: 208.2 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	2glj
沉积日期 deposition_date	2006-04-04
结构标题 title	crystal structure of aminopeptidase I from Clostridium acetobutylicum
关键词 keywords	;aminopeptidase I, NYSGXRC, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, HYDROLASE ;; HYDROLASE
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	77.74 Å
回转半径 Rg (电子) rg_electron	78.05 Å
零角强度 I(0) i0	20538000000.00
分子量 molecular_weight	1227500.0 kDa
排除体积 excluded_volume	1537700 Å³
包络体积 envelope_volume	2123400 Å³
水化壳体积 shell_volume	219140 Å³
包络直径 envelope_diameter	274.9 Å
壳层 Rg shell_rg	80.23 Å
包络 Rg envelope_rg	76.65 Å
形状 Rg shape_rg	78.04 Å
总 Rg total_rg	78.09 Å
总原子数 total_atoms	85992
残基数 n_residues	10920
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	208.2 Å
Rg (实空间) rg_real	75.45 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	2.0020e+10
I(0) 误差 (实空间) i0_real_error	3.4940e+08
Rg (倒空间) rg_reciprocal	76.89 Å
I(0) (倒空间) i0_reciprocal	20490000000.0000
解质量估计 total_estimate	0.8610
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	83.3 Å
偏度 Skewness skewness	0.361
峰度 Kurtosis kurtosis	-0.575
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.1217
最高正则化参数 α highest_alpha	2446000000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 0.979; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.012

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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 (3)

Entity 1 polymer

描述 description	Probable M18-family aminopeptidase 1
分子量 formula_weight	51664.6 kDa
EC 编号 ec_number	3.4.11.-
来源方法 src_method	man
拷贝数 entity_count	24

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
原子数 atom_count	91225

LLKEYKNAWDKYDDKQLKEVFALGDRFKNFISNCKTERECVTELIKTAEKSGYRNIEDILAKGETLKEGDKVYANNRGKGLIMFLIGKEPLYTGFKILGAHIDSPRLDLKQNPLYEDTDLAMLETHYYGGIKKYQWVTLPLAIHGVIVKKDGTIVNVCVGEDDNDPVFGVSDILVHLASEQLEKKASKVIEGEDLNILIGSIPLKDGEEKQKVKHNIMKILNEKYDISEEDFVSAELEIVPAGKARDYGFDRSMVMGYGQDDRICAYTSFEAMLEMKNAKKTCITILVDKEEVGSIGATGMQSKFFENTVADIMSLCGDYDELKLRKALYNSEMLSSDVSAAFDPNYPNVMEKRNSAYLGKGIVFNKYTGSRGKSGCNDANPEYIAELRRILSKESVNWQTAELGKVDQGGGGTIAYILAEYGMQVIDCGVALLNMHAPWEISSKADIYETKNGYSAFLNN

来源 Source

来源生物 organism	Clostridium acetobutylicum
NCBI 分类编号 ncbi_taxonomy_id	1488
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	48

Entity 3 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	5233

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6. 折叠分类 (SCOP + CATH) 48 domains

CATH v4.4 (48 domains)

结构域编号 domain_id	2gljA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljF02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljG02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljH02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljI02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljJ02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljK02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljL02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljM01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljM02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljN01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljN02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljO01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljO02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljP01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljP02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljQ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljQ02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljR01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljR02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljS01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljS02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljT01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljT02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljU01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljU02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljV01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljV02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljW01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljW02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

结构域编号 domain_id	2gljX01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	2gljX02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	250 — Aminopeptidase i, Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	121.708 Å
晶胞边长 b length_b	129.680 Å
晶胞边长 c length_c	222.728 Å
晶胞夹角 α angle_alpha	89.88 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	116.68 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	19.950 Å
R 因子 r_factor	0.2500
R_work r_work	0.2500
R_free r_free	0.2970

crystal structure of aminopeptidase I from Clostridium acetobutylicum

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