5B7Z

Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Ni2+

> 概要

5B7Z の概要

関連するPDBエントリー5B7Y 5B80
分子名称Uncharacterized protein TM_0416, (4S)-2-METHYL-2,4-PENTANEDIOL, NICKEL (II) ION, ... (5 entities in total)
機能のキーワードepimerase, ni2+, hyperthermophilic, eubacterium, isomerase
由来する生物種Thermotoga maritima MSB8
ポリマー鎖数2
分子量合計67072.44
構造登録者
Cao, T.P.,Shin, S.M.,Lee, D.W.,Lee, S.H. (登録日: 2016-06-10, 公開日: 2017-03-15)
主引用文献
Shin, S.M.,Cao, T.P.,Choi, J.M.,Kim, S.B.,Lee, S.J.,Lee, S.H.,Lee, D.W.
TM0416 Is a Hyperthermophilic Promiscuous Non-phosphorylated Sugar Isomerase That Catalyzes Various C5 and C6 Epimerization Reactions
Appl. Environ. Microbiol., 2017
PubMed: 28258150 (主引用文献が同じPDBエントリー)
DOI: 10.1128/AEM.03291-16
MImport into Mendeley
実験手法
X-RAY DIFFRACTION (1.5 Å)
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構造検証レポート

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.19670.6%0.7%1.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution
検証レポート(詳細版)をダウンロード

他の静止画像(非対称単位)

Molmil generated image of 5b7z
回転なし
Molmil generated image of 5b7z
x軸(左右方向)周りに90°回転
Molmil generated image of 5b7z
y軸(上下方向)周りに90°回転

> 構造情報

エンティティ

鎖名説明種類鎖長分子量分子数データベース名(アクセス番号)由来する生物種エンティティの一般名
A, BUncharacterized protein TM_0416polymer29032677.52
UniProt (Q9WYP7)
Pfam (PF01261)
Thermotoga maritima MSB8L-Ketose-3-Epimerase
(4S)-2-METHYL-2,4-PENTANEDIOLnon-polymer118.25
NICKEL (II) IONnon-polymer58.72
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOLnon-polymer252.34
waterwater18.0670

配列ビューア

非対称単位の内容

ポリマー鎖の数2
分子量合計65355.0
非ポリマー*分子数11
分子量合計1717.5
全て*分子量合計67072.4
*水分子は含んでいません

> 実験情報

精密化の統計情報

実験手法:X-RAY DIFFRACTION (1.5 Å)

格子定数 [Å]50.22555.22058.693
格子定数 [度]107.16102.2392.35
空間群P 1
分解能 [Å] (低 - 高)41.51 - 1.50
最も高い分解能シェルの値1.514 - 1.497
R因子0.1735
R-work0.17220
最も高い分解能シェルの値0.219
R-free0.19720
最も高い分解能シェルの値0.282
結合長の平均二乗偏差(RMSD) [Å]0.007
結合角の平均二乗偏差(RMSD) [度]1.112

回折データの統計情報

分解能 [Å] (低 - 高)50.00 - 1.50
最も高い分解能シェルの値 -
独立反射数90302
完全性 [%]96.0
冗長性3.5
最も高い分解能シェルの値3.3

結晶化条件

結晶ID方法pHpHの範囲温度単位
1VAPOR DIFFUSION, HANGING DROP6293

結晶化試薬

ID結晶ID濃度試薬名濃度 (単位)詳細
文献の結晶化試薬*
ID結晶ID溶液試薬名濃度 (単位) (単位)詳細
注釈情報は下記文献より抽出しています*

> 機能情報

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GO(遺伝子オントロジー)由来の情報

鎖名GO(遺伝子オントロジー)id名前空間内容
A0016853molecular_functionisomerase activity
A0046872molecular_functionmetal ion binding
A0006020biological_processinositol metabolic process
B0016853molecular_functionisomerase activity
B0046872molecular_functionmetal ion binding
B0006020biological_processinositol metabolic process
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PDBデータベースに由来する情報

site_id残基数詳細
AC16binding site for residue MPD A 301
鎖名残基
AARG117
AARG153
ATHR156
AASP157
AHOH451
AHOH549

AC26binding site for residue MPD A 302
鎖名残基
ALYS97
AGLU100
AVAL101
AMET104
AHOH416
B1PG304

AC34binding site for residue MPD A 303
鎖名残基
AARG214
ACYS244
ALEU245
AHOH480

AC44binding site for residue MPD A 304
鎖名残基
ALYS89
AILE92
AARG136
B1PG303

AC55binding site for residue NI A 305
鎖名残基
AGLU149
AASP182
AHIS208
AGLU243
AHOH429

AC65binding site for residue 1PG A 306
鎖名残基
ALEU108
ALYS145
AASN175
ATYR205
AARG238

AC710binding site for residue 1PG A 307
鎖名残基
AMET1
AGLY34
AGLN36
AGLU125
AGLU128
ALEU129
APHE259
ALYS263
AILE266
AILE267

AC83binding site for residue MPD B 301
鎖名残基
BARG214
BGLU243
BHOH654

AC95binding site for residue NI B 302
鎖名残基
BGLU149
BASP182
BHIS208
BGLU243
BHOH418

AD110binding site for residue 1PG B 303
鎖名残基
ALEU140
AMPD304
BGLY106
BLEU108
BHIS143
BLYS145
BASN175
BTYR205
BARG238
BHOH496

AD211binding site for residue 1PG B 304
鎖名残基
AGLU100
AMPD302
BLEU169
BASN173
BSER174
BASN175
BVAL177
BGLU202
BLYS203
BTYR205
BHOH651

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「HETATM」原子の座標から抽出されたリガンド結合部位

site_id残基数詳細
1PG_5b7z_A_30792-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL binding site
鎖名残基ligand
AMET1-LEU31PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AGLY341PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AGLN361PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
APHE2591PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ALYS2631PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AILE266-ILE2671PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

MPD_5b7z_A_3027(4S)-2-METHYL-2,4-PENTANEDIOL binding site
鎖名残基ligand
APRO45-SER46MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
ATRP50MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
ALYS97MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AGLU100-VAL101MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AMET104MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_5b7z_A_3047(4S)-2-METHYL-2,4-PENTANEDIOL binding site
鎖名残基ligand
ALYS89MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AILE92-GLU93MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AARG136MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
ALEU140MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BGLY106MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BHIS143MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

1PG_5b7z_B_303142-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL binding site
鎖名残基ligand
AGLU931PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AVAL961PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AGLU1001PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AGLU139-LEU1401PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BGLY106-LEU1081PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BHIS143-LYS1451PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BASN1751PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BTYR2051PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BARG2381PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

1PG_5b7z_B_304112-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL binding site
鎖名残基ligand
AGLU1001PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BLEU169-ARG1701PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BASN173-ASN1751PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BVAL177-GLY1781PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BGLU202-LYS2031PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
BTYR2051PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

1PG_5b7z_A_30672-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL binding site
鎖名残基ligand
AGLY1061PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ALEU1081PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ALYS1451PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AASN175-ARG1761PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ATYR2051PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
AARG2381PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

MPD_5b7z_A_3017(4S)-2-METHYL-2,4-PENTANEDIOL binding site
鎖名残基ligand
AARG117MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AGLU119MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AARG153-ASP157MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_5b7z_A_3034(4S)-2-METHYL-2,4-PENTANEDIOL binding site
鎖名残基ligand
AARG214MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AGLU243-LEU245MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_5b7z_B_3014(4S)-2-METHYL-2,4-PENTANEDIOL binding site
鎖名残基ligand
BARG214MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BGLU243-LEU245MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

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UniProtにおけるモチーフ・データベースPROSITEからの機能情報

site_id残基数詳細
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SwissProt/UniProtに記載されている蛋白質分子機能情報

site_id残基数詳細
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CSAにおける酵素触媒機能の情報

site_id残基数詳細

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