1m2v

Crystal Structure of the yeast Sec23/24 heterodimer

Method: X-RAY DIFFRACTION D_max: 146.7 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	1m2v
沉积日期 deposition_date	2002-06-25
结构标题 title	Crystal Structure of the yeast Sec23/24 heterodimer
关键词 keywords	zinc-finger, beta barrel, vWA domain, gelsolin domain, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	46.58 Å
回转半径 Rg (电子) rg_electron	46.87 Å
零角强度 I(0) i0	382441000.00
分子量 molecular_weight	163600.0 kDa
排除体积 excluded_volume	205580 Å³
包络体积 envelope_volume	276700 Å³
水化壳体积 shell_volume	51679 Å³
包络直径 envelope_diameter	158.8 Å
壳层 Rg shell_rg	47.16 Å
包络 Rg envelope_rg	46.98 Å
形状 Rg shape_rg	46.86 Å
总 Rg total_rg	46.90 Å
总原子数 total_atoms	11508
残基数 n_residues	1453
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	146.7 Å
Rg (实空间) rg_real	47.08 Å
Rg 误差 (实空间) rg_real_error	1.29 Å
I(0) (实空间) i0_real	3.8240e+08
I(0) 误差 (实空间) i0_real_error	7.1410e+06
Rg (倒空间) rg_reciprocal	46.59 Å
I(0) (倒空间) i0_reciprocal	382200000.0000
解质量估计 total_estimate	0.7819
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	38.8 Å
偏度 Skewness skewness	0.440
峰度 Kurtosis kurtosis	-0.736
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	42290000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.801; Smooth: 0.014

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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	protein transport protein SEC23
分子量 formula_weight	85463.2 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	11577

MDFETNEDINGVRFTWNVFPSTRSDANSNVVPVGCLYTPLKEYDELNVAPYNPVVCSGPHCKSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPVTVPPIFFFVVDLTSETENLDSLKESIITSLSLLPPNALIGLITYGNVVQLHDLSSETIDRCNVFRGDREYQLEALTEMLTGQKPTGPGGAASHLPNAMNKVTPFSLNRFFLPLEQVEFKLNQLLENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCYKNIPARIILFASGPGTVAPGLIVNSELKDPLRSHHDIDSDHAQHYKKACKFYNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQLTDSTGGVLLLTDAFSTAIFKQSYLRLFAKDEEGYLKMAFNGNMAVKTSKDLKVQGLIGHASAVKKTDANNISESEIGIGATSTWKMASLSPYHSYAIFFEIANTAANSNPMMSAPGSADRPHLAYTQFITTYQHSSGTNRIRVTTVANQLLPFGTPAIAASFDQEAAAVLMARIAVHKAETDDGADVIRWLDRTLIKLCQKYADYNKDDPQSFRLAPNFSLYPQFTYYLRRSQFLSVFNNSPDETAFYRHIFTREDTTNSLIMIQPTLTSFSMEDDPQPVLLDSISVKPNTILLLDTFFFILIYHGEQIAQWRKAGYQDDPQYADFKALLEEPKLEAAELLVDRFPLPRFIDTEAGGSQARFLLSKLNPSDNYQDMARGGSTIVLTDDVSLQNFMTHLQQVAVSGQA

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	protein transport protein SEC24
分子量 formula_weight	103733.2 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

MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPLNEDGLIVRCRRCRSYMNPFVTFIEQGRRWRCNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCAVMEYMAPKEYTLRQPPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIPNHDERTRISILCVDNAIHYFKIPLDSENNEESADQINMMDIADLEEPFLPRPNSMVVSLKACRQNIETLLTKIPQIFQSNLITNFALGPALKSAYHLIGGVGGKIIVVSGTLPNLGIGKLQRRNESGVVNTSKETAQLLSCQDSFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQTHFYPGFSGKNPNDIVKFSTEFAKHISMDFCMETVMRARGSTGLRMSRFYGHFFNRSSDLCAFSTMPRDQSYLFEVNVDESIMADYCYVQVAVLLSLNNSQRRIRIITLAMPTTESLAEVYASADQLAIASFYNSKAVEKALNSSLDDARVLINKSVQDILATYKKEIVVSNTAGGAPLRLCANLRMFPLLMHSLTKHMAFRSGIVPSDHRASALNNLESLPLKYLIKNIYPDVYSLHDMADEAGLPVQTEDGEATGTIVLPQPINATSSLFERYGLYLIDNGNELFLWMGGDAVPALVFDVFGTQDIFDIPIGKQEIPVVENSEFNQRVRNIINQLRNHDDVITYQSLYIVRGASLSEPVNHASAREVATLRLWASSTLVEDKILNNESYREFLQIMKARISK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 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 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	69

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1m2va1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.71 — ERP29 C domain-like
超家族 Superfamily superfamily	a.71.2 — Helical domain of Sec23/24
家族 Family family	a.71.2.1 — Helical domain of Sec23/24

结构域编号 domain_id	d1m2va2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.8 — beta-sandwich domain of Sec23/24
家族 Family family	b.2.8.1 — beta-sandwich domain of Sec23/24

结构域编号 domain_id	d1m2va3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.62 — vWA-like
超家族 Superfamily superfamily	c.62.1 — vWA-like
家族 Family family	c.62.1.2 — Trunk domain of Sec23/24

结构域编号 domain_id	d1m2va4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.109 — Gelsolin-like
超家族 Superfamily superfamily	d.109.2 — C-terminal, gelsolin-like domain of Sec23/24
家族 Family family	d.109.2.1 — C-terminal, gelsolin-like domain of Sec23/24

结构域编号 domain_id	d1m2va5
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.10 — Zn-finger domain of Sec23/24
家族 Family family	g.41.10.1 — Zn-finger domain of Sec23/24

结构域编号 domain_id	d1m2vb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.71 — ERP29 C domain-like
超家族 Superfamily superfamily	a.71.2 — Helical domain of Sec23/24
家族 Family family	a.71.2.1 — Helical domain of Sec23/24

结构域编号 domain_id	d1m2vb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.8 — beta-sandwich domain of Sec23/24
家族 Family family	b.2.8.1 — beta-sandwich domain of Sec23/24

结构域编号 domain_id	d1m2vb3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.62 — vWA-like
超家族 Superfamily superfamily	c.62.1 — vWA-like
家族 Family family	c.62.1.2 — Trunk domain of Sec23/24

结构域编号 domain_id	d1m2vb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.109 — Gelsolin-like
超家族 Superfamily superfamily	d.109.2 — C-terminal, gelsolin-like domain of Sec23/24
家族 Family family	d.109.2.1 — C-terminal, gelsolin-like domain of Sec23/24

结构域编号 domain_id	d1m2vb5
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.10 — Zn-finger domain of Sec23/24
家族 Family family	g.41.10.1 — Zn-finger domain of Sec23/24

CATH v4.4 (10 domains)

结构域编号 domain_id	1m2vA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1670 — beta-sandwich domain of Sec23/24

结构域编号 domain_id	1m2vA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	380 — Zn-finger domain of Sec23/24

结构域编号 domain_id	1m2vA03
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	410 — von Willebrand factor, type A domain

结构域编号 domain_id	1m2vA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	730 — Sec23/Sec24 helical domain

结构域编号 domain_id	1m2vA05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	20 — Severin
同源超家族 H-superfamily homologous superfamily	10 — Severin

结构域编号 domain_id	1m2vB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	730 — Sec23/Sec24 helical domain

结构域编号 domain_id	1m2vB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1670 — beta-sandwich domain of Sec23/24

结构域编号 domain_id	1m2vB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	380 — Zn-finger domain of Sec23/24

结构域编号 domain_id	1m2vB04
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	410 — von Willebrand factor, type A domain

结构域编号 domain_id	1m2vB05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	20 — Severin
同源超家族 H-superfamily homologous superfamily	10 — Severin

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7. 引用文献 (1)

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晶胞边长 a length_a	90.309 Å
晶胞边长 b length_b	126.371 Å
晶胞边长 c length_c	180.200 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	4

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	2.750 Å
最低分辨率 resolution_low	19.960 Å
R 因子 r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2570

fit	/app/data/saxs_computation/m2/1m2v/1m2v.fit
pddf	/app/data/pr_computation/m2/1m2v/1m2v.pr.out
profile	/app/data/saxs_computation/m2/1m2v/1m2v.dat

Crystal Structure of the yeast Sec23/24 heterodimer

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) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)