1nt9

Complete 12-subunit RNA polymerase II

Method: X-RAY DIFFRACTION D_max: 165.5 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	1nt9
沉积日期 deposition_date	2003-01-29
结构标题 title	Complete 12-subunit RNA polymerase II
关键词 keywords	;DNA-dependent RNA polymerase; cellular RNA polymerase; multisubunit complex; transcription; gene expression; mRNA; messenger RNA synthesis, TRANSCRIPTION, TRANSFERASE ;; TRANSCRIPTION, 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	50.54 Å
回转半径 Rg (电子) rg_electron	50.13 Å
零角强度 I(0) i0	2600450000.00
分子量 molecular_weight	427840.0 kDa
排除体积 excluded_volume	524610 Å³
包络体积 envelope_volume	537360 Å³
水化壳体积 shell_volume	91451 Å³
包络直径 envelope_diameter	161.1 Å
壳层 Rg shell_rg	54.04 Å
包络 Rg envelope_rg	47.02 Å
形状 Rg shape_rg	50.03 Å
总 Rg total_rg	50.22 Å
总原子数 total_atoms	—
残基数 n_residues	—
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	165.5 Å
Rg (实空间) rg_real	50.36 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	2.6000e+09
I(0) 误差 (实空间) i0_real_error	4.8140e+07
Rg (倒空间) rg_reciprocal	50.68 Å
I(0) (倒空间) i0_reciprocal	2602000000.0000
解质量估计 total_estimate	0.6537
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	64.0 Å
偏度 Skewness skewness	0.179
峰度 Kurtosis kurtosis	-0.395
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0016
最高正则化参数 α highest_alpha	274800000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 0.029; Positv: 1.000; Valcen: 0.983; Smooth: 0.890

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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 (12)

Entity 1 polymer

描述 description	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
分子量 formula_weight	191821.6 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
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	3779

MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

Entity 2 polymer

描述 description	DNA-directed polymerase II SECOND LARGEST SUBUNIT
分子量 formula_weight	138937.3 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF

Entity 3 polymer

描述 description	DNA-directed RNA polymerase II 45 kDa polypeptide
分子量 formula_weight	35330.5 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW

Entity 4 polymer

描述 description	YEAST DNA-DIRECTED RNA POLYMERASE II 32 KD POLYPEPTIDE
分子量 formula_weight	25451.2 kDa
EC 编号 ec_number	2.7.7.6
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	D

MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

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 5 polymer

描述 description	DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
分子量 formula_weight	25117.1 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E

MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Entity 6 polymer

描述 description	DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
分子量 formula_weight	17931.8 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F

MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Entity 7 polymer

描述 description	DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE
分子量 formula_weight	19081.1 kDa
EC 编号 ec_number	2.7.7.6
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	G

MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

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 8 polymer

描述 description	DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KD POLYPEPTIDE
分子量 formula_weight	16525.4 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR

Entity 9 polymer

描述 description	DNA-directed RNA polymerase II 14.2 kDa polypeptide
分子量 formula_weight	14308.2 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I

MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS

Entity 10 polymer

描述 description	DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide
分子量 formula_weight	8290.7 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J

MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD

Entity 11 polymer

描述 description	DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDE
分子量 formula_weight	13633.5 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K

MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Entity 12 polymer

描述 description	DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
分子量 formula_weight	7730.0 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L

MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1nt9a_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9b_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9c_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9d_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9e_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9f_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9g_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9h_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9i_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9j_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9k_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

结构域编号 domain_id	d1nt9l_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.8 — RNA polymerase
超家族 Superfamily superfamily	i.8.1 — RNA polymerase
家族 Family family	i.8.1.1 — RNA polymerase

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7. 引用文献 (1)

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晶胞边长 a length_a	220.400 Å
晶胞边长 b length_b	391.400 Å
晶胞边长 c length_c	282.200 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	8

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	4.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/nt/1nt9/1nt9.fit
pddf	/app/data/pr_computation/nt/1nt9/1nt9.pr.out
profile	/app/data/saxs_computation/nt/1nt9/1nt9.dat

Complete 12-subunit RNA polymerase II

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 (12)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

来源 Source

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

Entity 12 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)