1zc6

;Crystal Structure of Putative N-acetylglucosamine Kinase from Chromobacterium violaceum. Northeast Structural Genomics Target Cvr23. ;

Method: X-RAY DIFFRACTION D_max: 102.7 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1zc6
沉积日期 deposition_date	2005-04-11
结构标题 title	;Crystal Structure of Putative N-acetylglucosamine Kinase from Chromobacterium violaceum. Northeast Structural Genomics Target Cvr23. ;
关键词 keywords	;N-acetylglucosamine kinase, NESG, Q7NU07_CHRVO, cvr23, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	31.37 Å
回转半径 Rg (电子) rg_electron	31.49 Å
零角强度 I(0) i0	62186700.00
分子量 molecular_weight	59701.0 kDa
排除体积 excluded_volume	73562 Å³
包络体积 envelope_volume	95739 Å³
水化壳体积 shell_volume	27455 Å³
包络直径 envelope_diameter	108.4 Å
壳层 Rg shell_rg	35.19 Å
包络 Rg envelope_rg	31.67 Å
形状 Rg shape_rg	31.46 Å
总 Rg total_rg	31.90 Å
总原子数 total_atoms	4182
残基数 n_residues	569
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	102.7 Å
Rg (实空间) rg_real	31.64 Å
Rg 误差 (实空间) rg_real_error	1.02 Å
I(0) (实空间) i0_real	6.2190e+07
I(0) 误差 (实空间) i0_real_error	1.0270e+06
Rg (倒空间) rg_reciprocal	31.53 Å
I(0) (倒空间) i0_reciprocal	62180000.0000
解质量估计 total_estimate	0.8330
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.2 Å
偏度 Skewness skewness	0.498
峰度 Kurtosis kurtosis	-0.323
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7889000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.786; Smooth: 0.381

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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 (2)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1zc6a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.5 — BadF/BadG/BcrA/BcrD-like

结构域编号 domain_id	d1zc6a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.5 — BadF/BadG/BcrA/BcrD-like

结构域编号 domain_id	d1zc6b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.5 — BadF/BadG/BcrA/BcrD-like

结构域编号 domain_id	d1zc6b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.5 — BadF/BadG/BcrA/BcrD-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1zc6A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1zc6A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1zc6B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1zc6B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	178.245 Å
晶胞边长 b length_b	178.245 Å
晶胞边长 c length_c	117.663 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	32

空间群 space_group	I 4 2 2
空间群编号 int_tables_number	97
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	29.420 Å
R 因子 r_factor	0.2410
R_work r_work	0.2410
R_free r_free	0.2670

描述 description	probable N-acetylglucosamine kinase
分子量 formula_weight	32060.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4266

;Crystal Structure of Putative N-acetylglucosamine Kinase from Chromobacterium violaceum. Northeast Structural Genomics Target Cvr23. ;

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Chromobacterium violaceum
NCBI 分类编号 ncbi_taxonomy_id	243365
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	84

fit	/app/data/saxs_computation/zc/1zc6/1zc6.fit
pddf	/app/data/pr_computation/zc/1zc6/1zc6.pr.out
profile	/app/data/saxs_computation/zc/1zc6/1zc6.dat