1pzf

T.gondii LDH1 ternary complex with APAD+ and oxalate

Method: X-RAY DIFFRACTION D_max: 92.6 Å Quality: EXCELLENT

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	1pzf
沉积日期 deposition_date	2003-07-10
结构标题 title	T.gondii LDH1 ternary complex with APAD+ and oxalate
关键词 keywords	APAD, Rossmann fold, tetramer, apicomplexa, OXIDOREDUCTASE; OXIDOREDUCTASE
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	31.43 Å
回转半径 Rg (电子) rg_electron	30.59 Å
零角强度 I(0) i0	324552000.00
分子量 molecular_weight	144360.0 kDa
排除体积 excluded_volume	180790 Å³
包络体积 envelope_volume	209970 Å³
水化壳体积 shell_volume	53527 Å³
包络直径 envelope_diameter	97.5 Å
壳层 Rg shell_rg	40.26 Å
包络 Rg envelope_rg	30.84 Å
形状 Rg shape_rg	30.60 Å
总 Rg total_rg	31.31 Å
总原子数 total_atoms	10072
残基数 n_residues	1248
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	92.6 Å
Rg (实空间) rg_real	31.18 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	3.2460e+08
I(0) 误差 (实空间) i0_real_error	4.2750e+06
Rg (倒空间) rg_reciprocal	31.29 Å
I(0) (倒空间) i0_reciprocal	324600000.0000
解质量估计 total_estimate	0.9064
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.8 Å
偏度 Skewness skewness	0.070
峰度 Kurtosis kurtosis	-0.587
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	174600000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.921

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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	lactate dehydrogenase
分子量 formula_weight	35740.5 kDa
EC 编号 ec_number	1.1.1.27
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10446

MAPALVQRRKKVAMIGSGMIGGTMGYLCALRELADVVLYDVVKGMPEGKALDLSHVTSVVDTNVSVRAEYSYEAALTGADCVIVTAGLTKVPGKPDSEWSRNDLLPFNSKIIREIGQNIKKYCPKTFIIVVTNPLDCMVKVMCEASGVPTNMICGMACMLDSGRFRRYVADALSVSPRDVQATVIGTHGDCMVPLVRYITVNGYPIQKFIKDGVVTEKQLEEIAEHTKVSGGEIVRFLGQGSAYYAPAASAVAMATSFLNDEKRVIPCSVYCNGEYGLKDMFIGLPAVIGGAGIERVIELELNEEEKKQFQKSVDDVMALNKAVAALQAPG

来源 Source

来源生物 organism	Toxoplasma gondii
NCBI 分类编号 ncbi_taxonomy_id	5811
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	OXALATE ION
分子量 formula_weight	88.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE
分子量 formula_weight	662.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	374

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1pzfa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1pzfa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

结构域编号 domain_id	d1pzfa3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1pzfb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1pzfb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

结构域编号 domain_id	d1pzfb3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1pzfc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1pzfc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

结构域编号 domain_id	d1pzfd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1pzfd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1pzfA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1pzfA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

结构域编号 domain_id	1pzfB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1pzfB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

结构域编号 domain_id	1pzfC01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1pzfC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

结构域编号 domain_id	1pzfD01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1pzfD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

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7. 引用文献 (1)

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晶胞边长 a length_a	68.065 Å
晶胞边长 b length_b	124.976 Å
晶胞边长 c length_c	86.686 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.09 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1775
R_work r_work	0.1775
R_free r_free	0.2176

fit	/app/data/saxs_computation/pz/1pzf/1pzf.fit
pddf	/app/data/pr_computation/pz/1pzf/1pzf.pr.out
profile	/app/data/saxs_computation/pz/1pzf/1pzf.dat