1ofd

Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom resolution

Method: X-RAY DIFFRACTION

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2

SYNECHOCYSTIS SP.

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白单体	单体	蛋白 1	FLAVIN MONONUCLEOTIDE × 1 FE3-S4 CLUSTER × 1 2-OXOGLUTARIC ACID × 1 water × 1	与蛋白数一致
2	蛋白单体	单体	蛋白 1	FLAVIN MONONUCLEOTIDE × 1 FE3-S4 CLUSTER × 1 2-OXOGLUTARIC ACID × 1 water × 1	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	GLTS_SYNY3
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–1520； UniProt 37–1556 作者链 B； PDB构建体 1–1520； UniProt 37–1556

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1ofd
沉积日期 deposition_date	2003-04-14
结构标题 title	Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom resolution
关键词 keywords	OXIDOREDUCTASE, COMPLEX ENZYME, SUBSTRATE CHANNELING, AMIDOTRANSFERASE, FLAVOPROTEIN, IRON-SULPHUR, FD-GOGAT; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

1ofd__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

1ofd__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

1ofd__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	33.46 Å
Rg（电子密度）	32.58 Å
总 Rg	33.18 Å
原子数	11482
残基数	1491
排除体积	204080 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`1ofd__assembly_1__model_1`	monomeric （1）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`1ofd__assembly_2__model_1`	monomeric （1）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2
分子量 formula_weight	165711.7 kDa
EC 编号 ec_number	1.4.7.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	24388

CGVGFIANLRGKPDHTLVEQALKALGCMEHRGGCSADNDSGDGAGVMTAIPRELLAQWFNTRNLPMPDGDRLGVGMVFLPQEPSAREVARAYVEEVVRLEKLTVLGWREVPVNSDVLGIQAKNNQPHIEQILVTCPEGCAGDELDRRLYIARSIIGKKLAEDFYVCSFSCRTIVYKGMVRSIILGEFYLDLKNPGYTSNFAVYHRRFSTNTMPKWPLAQPMRLLGHNGEINTLLGNINWMAAREKELEVSGWTKAELEALTPIVNQANSDSYNLDSALELLVRTGRSPLEAAMILVPEAYKNQPALKDYPEISDFHDYYSGLQEPWDGPALLVFSDGKIVGAGLDRNGLRPARYCITKDDYIVLGSEAGVVDLPEVDIVEKGRLAPGQMIAVDLAEQKILKNYQIKQQAAQKYPYGEWIKIQRQTVASDSFAEKTLFNDAQTVLQQQAAFGYTAEDVEMVVVPMASQGKEPTFCMGDDTPLAVLSHKPRLLYDYFKQRFAQVTNPPIDPLRENLVMSLAMFLGKRGNLLEPKAESARTIKLRSPLVNEVELQAIKTGQLQVAEVSTLYDLDGVNSLEDALTNLVKTAIATVQAGAEILVLTDRPNGAILTENQSFIPPLLAVGAVHHHLIRAGLRLKASLIVDTAQCWSTHHFACLVGYGASAICPYLALESVRQWWLDEKTQKLMENGRLDRIDLPTALKNYRQSVEAGLFKILSKMGISLLASYHGAQIFEAIGLGAELVEYAFAGTTSRVGGLTIADVAGEVMVFHGMAFPEMAKKLENFGFVNYRPGGEYHMNSPEMSKSLHKAVAAYKVGGNGNNGEAYDHYELYRQYLKDRPVTALRDLLDFNADQPAISLEEVESVESIVKRFCTGGMSLGALSREAHETLAIAMNRLGAKSNSGEGGEDVVRYLTLDDVDSEGNSPTLPHLHGLQNGDTANSAIKQIASGRFGVTPEYLMSGKQLEIKMAQGAKPGEGGQLPGKKVSEYIAMLRRSKPGVTLISPPPHHDIYSIEDLAQLIYDLHQINPEAQVSVKLVAEIGIGTIAAGVAKANADIIQISGHDGGTGASPLSSIKHAGSPWELGVTEVHRVLMENQLRDRVLLRADGGLKTGWDVVMAALMGAEEYGFGSIAMIAEGCIMARVCHTNNCPVGVATQQERLRQRFKGVPGQVVNFFYFIAEEVRSLLAHLGYRSLDDIIGRTDLLKVRSDVQLSKTQNLTLDCLLNLPDTKQNRQWLNHEPVHSNGPVLDDDILADPDIQEAINHQTTATKTYRLVNTDRTVGTRLSGAIAKKYGNNGFEGNITLNFQGAAGQSFGAFNLDGMTLHLQGEANDYVGKGMNGGEIVIVPHPQASFAPEDNVIIGNTCLYGATGGNLYANGRAGERFAVRNSVGKAVIEGAGDHCCEYMTGGVIVVLGPVGRNVGAGMTGGLAYFLDEVGDLPEKINPEIITLQRITASKGEEQLKSLITAHVEHTGSPKGKAILANWSDYLGKFWQAVPPSEKDSPEANNDVSLTGEKTLTSV

来源 Source

来源生物 organism	SYNECHOCYSTIS SP.
NCBI 分类编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	ESCHERICHIA COLI

实体 2 Entity 2 non-polymer

描述 description	FLAVIN MONONUCLEOTIDE
分子量 formula_weight	456.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 3 Entity 3 non-polymer

描述 description	FE3-S4 CLUSTER
分子量 formula_weight	295.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 4 Entity 4 non-polymer

描述 description	2-OXOGLUTARIC ACID
分子量 formula_weight	146.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 5 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	1424

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1ofda1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.80 — Single-stranded right-handed beta-helix
超家族 Superfamily superfamily	b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain
家族 Family family	b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain

结构域编号 domain_id	d1ofda2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
家族 Family family	c.1.4.1 — FMN-linked oxidoreductases

结构域编号 domain_id	d1ofda3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

结构域编号 domain_id	d1ofdb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.80 — Single-stranded right-handed beta-helix
超家族 Superfamily superfamily	b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain
家族 Family family	b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain

结构域编号 domain_id	d1ofdb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
家族 Family family	c.1.4.1 — FMN-linked oxidoreductases

结构域编号 domain_id	d1ofdb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

CATH v4.4 (8 domains)

结构域编号 domain_id	1ofdA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1ofdA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	1ofdA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	1ofdA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	20 — Pectate Lyase C-like
同源超家族 H-superfamily homologous superfamily	60 — Glutamate synthase, alpha subunit, C-terminal domain

结构域编号 domain_id	1ofdB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1ofdB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	1ofdB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	1ofdB04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	20 — Pectate Lyase C-like
同源超家族 H-superfamily homologous superfamily	60 — Glutamate synthase, alpha subunit, C-terminal domain

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晶胞边长 a length_a	125.017 Å
晶胞边长 b length_b	149.665 Å
晶胞边长 c length_c	195.926 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	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1940
R_work r_work	0.1920
R_free r_free	0.2310

Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom resolution

1. 蛋白身份与相关结构 Protein Identity & Related Structures

FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

1ofd__assembly_1__model_1

1ofd__assembly_1__model_1 | I(q)

1ofd__assembly_1__model_1 | P(r) · Pending

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. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom resolution

1. 蛋白身份与相关结构 Protein Identity & Related Structures

FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

1ofd__assembly_1__model_1

1ofd__assembly_1__model_1 | I(q)

1ofd__assembly_1__model_1 | P(r) · Pending

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. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)