1kfi

Crystal Structure of the Exocytosis-Sensitive Phosphoprotein, pp63/Parafusin (phosphoglucomutase) from Paramecium

Method: X-RAY DIFFRACTION D_max: 119.9 Å Quality: REASONABLE

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	1kfi
沉积日期 deposition_date	2001-11-21
结构标题 title	Crystal Structure of the Exocytosis-Sensitive Phosphoprotein, pp63/Parafusin (phosphoglucomutase) from Paramecium
关键词 keywords	parafusin, phosphoprotein pp63, exocytosis, ISOMERASE; ISOMERASE
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	35.36 Å
回转半径 Rg (电子) rg_electron	35.07 Å
零角强度 I(0) i0	248795000.00
分子量 molecular_weight	127590.0 kDa
排除体积 excluded_volume	159470 Å³
包络体积 envelope_volume	198190 Å³
水化壳体积 shell_volume	47492 Å³
包络直径 envelope_diameter	122.9 Å
壳层 Rg shell_rg	41.15 Å
包络 Rg envelope_rg	35.15 Å
形状 Rg shape_rg	35.09 Å
总 Rg total_rg	35.41 Å
总原子数 total_atoms	9002
残基数 n_residues	1140
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	119.9 Å
Rg (实空间) rg_real	36.80 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	2.4840e+08
I(0) 误差 (实空间) i0_real_error	3.2370e+06
Rg (倒空间) rg_reciprocal	35.41 Å
I(0) (倒空间) i0_reciprocal	248800000.0000
解质量估计 total_estimate	0.6772
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	34.6 Å
偏度 Skewness skewness	0.501
峰度 Kurtosis kurtosis	-0.326
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	2.8430
最高正则化参数 α highest_alpha	110800000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 0.894; Sysdev: 0.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.683

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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	phosphoglucomutase 1
分子量 formula_weight	63881.8 kDa
EC 编号 ec_number	5.4.2.2
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	9207

MQQVIPAPRVQVTQPYAGQKPGTSGLRKKVSEATQPNYLENFVQSIFNTLRKDELKPKNVLFVGGDGRYFNRQAIFSIIRLAYANDISEVHVGQAGLMSTPASSHYIRKVNEEVGNCIGGIILTASHNPGGKEHGDFGIKFNVRTGAPAPEDFTDQIYTHTTKIKEYLTVDYEFEKHINLDQIGVYKFEGTRLEKSHFEVKVVDTVQDYTQLMQKLFDFDLLKGLFSNKDFSFRFDGMHGVAGPYAKHIFGTLLGCSKESLLNCDPSEDFGGGHPDPNLTYAHDLVELLDIHKKKDVGTVPQFGAACDGDADRNMILGRQFFVTPSDSLAVIAANANLIFKNGLLGAARSMPTSGALDKVAAKNGIKLFETPTGWKFFGNLMDAGLINLCGEESFGTGSNHIREKDGIWAVLAWLTILAHKNKNTDHFVTVEEIVTQYWQQFGRNYYSRYDYEQVDSAGANKMMEHLKTKFQYFEQLKQGNKADIYDYVDPVDQSVSKNQGVRFVFGDGSRIIFRLSGTGSVGATIRIYFEQFEQQQIQHETATALANIIKLGLEISDIAQFTGRNEPTVIT

来源 Source

来源生物 organism	Paramecium tetraurelia
NCBI 分类编号 ncbi_taxonomy_id	5888
宿主生物 host_organism	Escherichia coli

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	2

Entity 3 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	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	205

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1kfia1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1kfia2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1kfia3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1kfia4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.2 — Phosphoglucomutase, C-terminal domain
家族 Family family	d.129.2.1 — Phosphoglucomutase, C-terminal domain

结构域编号 domain_id	d1kfib1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1kfib2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1kfib3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.84 — Phosphoglucomutase, first 3 domains
超家族 Superfamily superfamily	c.84.1 — Phosphoglucomutase, first 3 domains
家族 Family family	c.84.1.1 — Phosphoglucomutase, first 3 domains

结构域编号 domain_id	d1kfib4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.2 — Phosphoglucomutase, C-terminal domain
家族 Family family	d.129.2.1 — Phosphoglucomutase, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1kfiA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1kfiA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1kfiA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1kfiA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

结构域编号 domain_id	1kfiB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1kfiB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1kfiB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	120 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3

结构域编号 domain_id	1kfiB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	50 — Alpha-D-phosphohexomutase, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	67.346 Å
晶胞边长 b length_b	133.609 Å
晶胞边长 c length_c	150.545 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	8

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	2.400 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2270
R_free r_free	0.2860

fit	/app/data/saxs_computation/kf/1kfi/1kfi.fit
pddf	/app/data/pr_computation/kf/1kfi/1kfi.pr.out
profile	/app/data/saxs_computation/kf/1kfi/1kfi.dat