SAXSdb — 1zhh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1zhh
沉积日期 deposition_date	2005-04-25
结构标题 title	Crystal Structure of the Apo Form of Vibrio Harveyi LUXP Complexed with the Periplasmic Domain of LUXQ
关键词 keywords	;PERIPLASMIC BINDING PROTEIN, PER/ARNT/SIMPLE-MINDED (PAS) FOLD, AUTOINDUCER-2 (AI-2), QUORUM SENSING, SENSOR KINASE, Signaling Protein ;; SIGNALING PROTEIN
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	27.22 Å
回转半径 Rg (电子) rg_electron	26.34 Å
零角强度 I(0) i0	64555800.00
分子量 molecular_weight	62805.0 kDa
排除体积 excluded_volume	78595 Å³
包络体积 envelope_volume	97075 Å³
水化壳体积 shell_volume	30510 Å³
包络直径 envelope_diameter	89.0 Å
壳层 Rg shell_rg	33.69 Å
包络 Rg envelope_rg	26.36 Å
形状 Rg shape_rg	26.31 Å
总 Rg total_rg	27.22 Å
总原子数 total_atoms	4439
残基数 n_residues	552
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	85.3 Å
Rg (实空间) rg_real	27.14 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	6.4560e+07
I(0) 误差 (实空间) i0_real_error	9.6010e+05
Rg (倒空间) rg_reciprocal	27.17 Å
I(0) (倒空间) i0_reciprocal	64560000.0000
解质量估计 total_estimate	0.9098
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	30.9 Å
偏度 Skewness skewness	0.226
峰度 Kurtosis kurtosis	-0.531
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13120000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.979

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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	Autoinducer 2-binding periplasmic protein luxP
分子量 formula_weight	39295.0 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	4772

TQVLNGYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNITTPVREWDKHQPFLYVGFDHAEGSRELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGREDIMINGWGGGSAELDAIQKGDLDITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSDN

来源 Source

来源生物 organism	Vibrio harveyi
NCBI 分类编号 ncbi_taxonomy_id	669
宿主生物 host_organism	Escherichia coli BL21

Entity 2 polymer

描述 description	Autoinducer 2 sensor kinase/phosphatase luxQ
分子量 formula_weight	27407.7 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	B

GSYFSKQIIWQEVDRTKQQTSALIHNIFDSHFAAIQIHHDSNSKSEVIRDFYTDRDTDVLNFFFLSIDQSDPSHTPEFRFLTDHKGIIWDDGNAHFYGVNDLILDSLANRVSFSNNWYYINVMTSIGSRHMLVRRVPILDPSTGEVLGFSFNAVVLDNNFALMEKLKSESNVDNVVLVANSVPLANSLIGDEPYNVADVLQRKSSDKRLDKLLVIETPIVVNAVTTELCLLTVQDNQSVVTL

来源 Source

来源生物 organism	Vibrio harveyi
NCBI 分类编号 ncbi_taxonomy_id	669
宿主生物 host_organism	Escherichia coli BL21

Entity 3 non-polymer

描述 description	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
分子量 formula_weight	207.3 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	333

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1zhha_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

结构域编号 domain_id	d1zhhb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.3 — LuxQ-periplasmic domain-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1zhhA01
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	2300 — Response regulator

结构域编号 domain_id	1zhhA02
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	2300 — Response regulator

结构域编号 domain_id	1zhhB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	220 — LuxQ periplasmic domain, N-terminal subdomain

结构域编号 domain_id	1zhhB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	20 — Anthopleurin-A
同源超家族 H-superfamily homologous superfamily	100 — LuxQ periplasmic domain, C-terminal subdomain

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7. 引用文献 (1)

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晶胞边长 a length_a	128.468 Å
晶胞边长 b length_b	128.468 Å
晶胞边长 c length_c	95.671 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	1.940 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2070
R_work r_work	0.2060
R_free r_free	0.2220

fit	/app/data/saxs_computation/zh/1zhh/1zhh.fit
pddf	/app/data/pr_computation/zh/1zhh/1zhh.pr.out
profile	/app/data/saxs_computation/zh/1zhh/1zhh.dat

Crystal Structure of the Apo Form of Vibrio Harveyi LUXP Complexed with the Periplasmic Domain of LUXQ

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)