1h38

Structure of a T7 RNA polymerase elongation complex at 2.9A resolution

Method: X-RAY DIFFRACTION D_max: 200.6 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	1h38
沉积日期 deposition_date	2002-08-24
结构标题 title	Structure of a T7 RNA polymerase elongation complex at 2.9A resolution
关键词 keywords	;TRANSFERASE, RNA POLYMERASE, T7 RNA POLYMERASE, ELONGATION COMPLEX, PROTEIN/DNA/RNA, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS ;; TRANSFERASE
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	64.67 Å
回转半径 Rg (电子) rg_electron	65.57 Å
零角强度 I(0) i0	2870230000.00
分子量 molecular_weight	425340.0 kDa
排除体积 excluded_volume	521540 Å³
包络体积 envelope_volume	832520 Å³
水化壳体积 shell_volume	108540 Å³
包络直径 envelope_diameter	227.8 Å
壳层 Rg shell_rg	61.30 Å
包络 Rg envelope_rg	64.56 Å
形状 Rg shape_rg	65.56 Å
总 Rg total_rg	65.51 Å
总原子数 total_atoms	29786
残基数 n_residues	3565
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	200.6 Å
Rg (实空间) rg_real	65.25 Å
Rg 误差 (实空间) rg_real_error	1.70 Å
I(0) (实空间) i0_real	2.8700e+09
I(0) 误差 (实空间) i0_real_error	6.2600e+07
Rg (倒空间) rg_reciprocal	64.11 Å
I(0) (倒空间) i0_reciprocal	2864000000.0000
解质量估计 total_estimate	0.8305
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	66.8 Å
偏度 Skewness skewness	0.462
峰度 Kurtosis kurtosis	-0.522
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	171400000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.001

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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 (5)

Entity 1 polymer

描述 description	DNA-DIRECTED RNA POLYMERASE
分子量 formula_weight	98984.2 kDa
EC 编号 ec_number	2.7.7.6
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	30948

MNTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA

来源 Source

来源生物 organism	BACTERIOPHAGE T7
NCBI 分类编号 ncbi_taxonomy_id	10760
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	;5'-D(GPGPGPAPAPTPCPGPAPCP APTPCPGPCPCPGPC)-3' ;
分子量 formula_weight	5526.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	E,H,K,N

GGGAATCGACATCGCCGC

Entity 3 polymer

描述 description	;5'-R(APAPCPUPGPCPGPGPCPGP APU)-3' ;
分子量 formula_weight	3851.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	F,I,L,O

AACUGCGGCGAU

Entity 4 polymer

描述 description	5'-D(GPTPCPGPAPTPTPCPCPCP)-3'
分子量 formula_weight	2996.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	G,J,M,P

GTCGATTCCC

Entity 5 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	1162

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1h38a_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.3 — T7 RNA polymerase

结构域编号 domain_id	d1h38b_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.3 — T7 RNA polymerase

结构域编号 domain_id	d1h38c_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.3 — T7 RNA polymerase

结构域编号 domain_id	d1h38d_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.3 — T7 RNA polymerase

CATH v4.4 (20 domains)

结构域编号 domain_id	1h38A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1320 — T7 RNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — DNA-directed RNA polymerase, N-terminal domain

结构域编号 domain_id	1h38A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	260 —

结构域编号 domain_id	1h38A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	370 —

结构域编号 domain_id	1h38A04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	280 —

结构域编号 domain_id	1h38A05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	1h38B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1320 — T7 RNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — DNA-directed RNA polymerase, N-terminal domain

结构域编号 domain_id	1h38B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	260 —

结构域编号 domain_id	1h38B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	370 —

结构域编号 domain_id	1h38B04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	280 —

结构域编号 domain_id	1h38B05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	1h38C01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1320 — T7 RNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — DNA-directed RNA polymerase, N-terminal domain

结构域编号 domain_id	1h38C02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	260 —

结构域编号 domain_id	1h38C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	370 —

结构域编号 domain_id	1h38C04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	280 —

结构域编号 domain_id	1h38C05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	1h38D01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1320 — T7 RNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — DNA-directed RNA polymerase, N-terminal domain

结构域编号 domain_id	1h38D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	260 —

结构域编号 domain_id	1h38D03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	370 —

结构域编号 domain_id	1h38D04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	280 —

结构域编号 domain_id	1h38D05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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7. 引用文献 (1)

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晶胞边长 a length_a	79.907 Å
晶胞边长 b length_b	84.971 Å
晶胞边长 c length_c	202.003 Å
晶胞夹角 α angle_alpha	90.36 °
晶胞夹角 β angle_beta	92.97 °
晶胞夹角 γ angle_gamma	109.94 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	39.930 Å
R 因子 r_factor	0.2360
R_work r_work	0.2360
R_free r_free	0.2840

fit	/app/data/saxs_computation/h3/1h38/1h38.fit
pddf	/app/data/pr_computation/h3/1h38/1h38.pr.out
profile	/app/data/saxs_computation/h3/1h38/1h38.dat

Structure of a T7 RNA polymerase elongation complex at 2.9A resolution

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (4 domains)

CATH v4.4 (20 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)