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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1qki | |||||||||
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タイトル | X-RAY STRUCTURE OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE (VARIANT CANTON R459L) COMPLEXED WITH STRUCTURAL NADP+ | |||||||||
![]() | GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE | |||||||||
![]() | OXIDOREDUCTASE / OXIDOREDUTASE / (CHOH(D)-NADP) / GLUCOSE METABOLISM | |||||||||
機能・相同性 | ![]() negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration ...negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP+ metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / cholesterol biosynthetic process / erythrocyte maturation / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / TP53 Regulates Metabolic Genes / : / lipid metabolic process / centriolar satellite / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Au, S.W.N. / Gover, S. / Lam, V.M.S. / Adams, M.J. | |||||||||
![]() | ![]() タイトル: Human Glucose-6-Phosphate Dehydrogenase: The Crystal Structure Reveals a Structural Nadp+ Molecule and Provides Insights Into Enzyme Deficiency 著者: Au, S.W.N. / Gover, S. / Lam, V.M.S. / Adams, M.J. #1: ジャーナル: Acta Crystallogr.,Sect.D / 年: 1999 タイトル: Solution of the Structure of Tetrameric Human Glucose 6-Phosphate Dehydrogenase by Molecular Replacement 著者: Au, S.W.N. / Naylor, C.E. / Gover, S. / Vandeputte-Rutten, L. / Scopes, D.A. / Mason, P.J. / Luzzatto, L. / Lam, V.M.S. / Adams, M.J. | |||||||||
履歴 |
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Remark 650 | HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO THE 2.0A LEUCONOSTOC ... HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO THE 2.0A LEUCONOSTOC MESENTERODES STRUCTURE, 1DPG. THE BEND AT LYS 47 IN HELIX A OF ALL SUBUNITS IS A CONSEQUENCE OF THE CONSERVED PRO 50. | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: PROCHECK WITH EXTENSION TAKEN WHERE HYDROGEN BONDING INDICATES THAT ... SHEET DETERMINATION METHOD: PROCHECK WITH EXTENSION TAKEN WHERE HYDROGEN BONDING INDICATES THAT THIS IS APPROPRIATE |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 768.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 635.2 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 1dpgS S: 精密化の開始モデル |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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詳細 | THERE ARE TWO TETRAMERS ABCD AND EFGH IN THE ASYMMETRICUNIT; THESE ARE RELATED BY NON-CRYSTALLOGRAPHY SYMMETRY.DUE TO THE DIFFERENCE OF HINGE ANGLE IN EVERY SUBUNIT, TWOMATRICES ARE PROVIDED TO GENERATE A WHOLE SUBUNIT - ONEFOR THE COENZYME DOMAIN (RESIDUES 31- 200) AND ANOTHER FORTHE LARGE DOMAIN (RESIDUE 201 -511). PRO 172 IS ONLY INTHE CIS CONFORMATION IN SUBUNIT E. |
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要素
#1: タンパク質 | 分子量: 59167.367 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+) #2: 化合物 | ChemComp-NAP / #3: 化合物 | ChemComp-GOA / #4: 化合物 | ChemComp-GOL / #5: 水 | ChemComp-HOH / | 構成要素の詳細 | AS ALL THE EIGHT SUBUNITS ARE VERY SIMILAR, ONLY THE SALT BRIDGES WITHIN SUBUNIT A AND WITHIN ...AS ALL THE EIGHT SUBUNITS ARE VERY SIMILAR, ONLY THE SALT BRIDGES WITHIN SUBUNIT A AND WITHIN SUBUNIT E ARE GIVEN. FOR DETAILS OF RESIDUES FORMING INTERSUBUN | 由来についての詳細 | THE G6PD PROTEIN USED IN THIS WORK IS THE NATURAL VARIANT ARG459 -> LEU (CANTON, CLASS II, FREQUENT IN CHINA). | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 3.04 Å3/Da / 溶媒含有率: 59.5 % / 解説: 3 DATA SETS WERE MERGED, SEE REFERENCE 1. | ||||||||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.8 詳細: HANGING DROP VAPOUR DIFFUSION. 1+1 MICROLITER DROPS IN THE WELL 0.1M SODIUM CITRATE, 0.05M GLYCOLIC ACID, PH 5.8. PROTEIN CONCENTRATION 10MG/ML | ||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法詳細: used microseeding, Au, S.W.N., (1999) Acta Crystallogr.,Sect.D, 55, 826. pH: 5.8 | ||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K | |||||||||
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放射光源 | 由来: ![]() ![]() ![]() | |||||||||
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1997年2月15日 / 詳細: MIRRORS | |||||||||
放射 | モノクロメーター: GRAPHITE(002) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray | |||||||||
放射波長 |
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反射 | 解像度: 3→25 Å / Num. obs: 98864 / % possible obs: 85.3 % / Observed criterion σ(I): 4 / 冗長度: 2.2 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 5.2 | |||||||||
反射 シェル | 解像度: 3→3.2 Å / 冗長度: 1.8 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.565 / % possible all: 74.7 | |||||||||
反射 | *PLUS Num. measured all: 647973 | |||||||||
反射 シェル | *PLUS 最低解像度: 3.05 Å / % possible obs: 72 % / Rmerge(I) obs: 0.565 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 1DPG 解像度: 3→25 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / 交差検証法: FREE R-VALUE / σ(F): 0 詳細: LITTLE OF THE N-TERMINAL TAIL IS SEEN IN THE ELECTRON DENSITY MAP; SEGMENTS BUILT HERE VARY IN LENGTH AND CONFORMATION IN EACH SUBUNIT AND DO NOT OBEY THE NON-CRYSTALLOGRAPHIC SYMMETRY. FOR ...詳細: LITTLE OF THE N-TERMINAL TAIL IS SEEN IN THE ELECTRON DENSITY MAP; SEGMENTS BUILT HERE VARY IN LENGTH AND CONFORMATION IN EACH SUBUNIT AND DO NOT OBEY THE NON-CRYSTALLOGRAPHIC SYMMETRY. FOR DETAILS OF THE RESIDUES RESTRAINED IN NCS GROUPS 1 AND 2, SEE JRNL REFERENCE. PARAMETER FILES FOR GLYCOLATE AND GLYCEROL ARE COMBINED INTO ONE FILE. TOPOLOGY FILES FOR GLYCOLATE AND GLYCEROL ARE COMBINED INTO ONE FILE.
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Refine analyze | Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.57 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3→25 Å
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拘束条件 |
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Refine LS restraints NCS | Rms dev Biso : 3.21 Å2 / Rms dev position: 0.84 Å / Weight Biso : 1 / Weight position: 50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 3→3.05 Å / Total num. of bins used: 20
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Xplor file |
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ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor obs: 0.405 |