- PDB-2kpt: Solution NMR structure of the N-terminal domain of cg2496 protein... -
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基本情報
登録情報
データベース: PDB / ID: 2kpt
タイトル
Solution NMR structure of the N-terminal domain of cg2496 protein from Corynebacterium glutamicum. Northeast Structural Genomics Consortium Target CgR26A
要素
Putative secreted protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / methods development / alpha/beta / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
機能・相同性
Diaminopimelate Epimerase; Chain A, domain 1 - #50 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / :
0.9 mM [U-100% 13C; U-100% 15N] cgr26a, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.9 mM [U-5% 13C; U-100% 15N] cgr26a, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O
90% H2O/10% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
0.9mM
cgr26a-1
[U-100% 13C; U-100% 15N]
1
20mM
MES-2
1
200mM
sodium chloride-3
1
5mM
calcium chloride-4
1
50uM
DSS-5
1
0.02 %
sodium azide-6
1
0.9mM
cgr26a-7
[U-100% 13C; U-100% 15N]
2
20mM
MES-8
2
200mM
sodium chloride-9
2
5mM
calcium chloride-10
2
50uM
DSS-11
2
0.02 %
sodium azide-12
2
0.9mM
cgr26a-13
[U-5% 13C; U-100% 15N]
3
20mM
MES-14
3
200mM
sodium chloride-15
3
5mM
calcium chloride-16
3
50uM
DSS-17
3
0.02 %
sodium azide-18
3
試料状態
イオン強度: 225 / pH: 6.5 / 圧: ambient / 温度: 298 K
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NMR測定
NMRスペクトロメーター
タイプ
製造業者
モデル
磁場強度 (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
600
1
Bruker Avance
Bruker
AVANCE
800
2
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解析
NMR software
名称
バージョン
開発者
分類
VnmrJ
2.1B
Varian
collection
TopSpin
2.1
BrukerBiospin
collection
TopSpin
2.1
BrukerBiospin
解析
PROSA
6.4
Guntert
解析
XEASY
1.3.13
Bartelsetal.
データ解析
CARA
1.8.4
KellerandWuthrich
データ解析
CARA
1.8.4
KellerandWuthrich
chemicalshiftassignment
CARA
1.8.4
KellerandWuthrich
peakpicking
PINE
1
Bahrami, Markley, Assadi, andEghbalnia
chemicalshiftassignment
TALOS+
1.2009.0721.18
Shen, Cornilescu, DelaglioandBax
データ解析
CYANA
2.1
Guntert, MumenthalerandWuthrich
構造決定
AutoStructure
2.2.1
Huang, Tejero, PowersandMontelione
構造決定
AutoStructure
2.2.1
Huang, Tejero, PowersandMontelione
structurevalidation
PSVS
1.4
BhattacharyaandMontelione
structurevalidation
CNS
1.2.1
Brunger, Adams, Clore, Gros, NilgesandRead
精密化
精密化
手法: simulated annealing / ソフトェア番号: 1 詳細: Structure determination was performed iteratively with CYANA v2.1 using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the ...詳細: Structure determination was performed iteratively with CYANA v2.1 using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraints
NOE constraints total: 2819 / NOE intraresidue total count: 486 / NOE long range total count: 1072 / NOE medium range total count: 615 / NOE sequential total count: 646 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 73 / Protein psi angle constraints total count: 73
代表構造
選択基準: lowest energy
NMRアンサンブル
Average torsion angle constraint violation: 0.05 ° / コンフォーマー選択の基準: target function / 計算したコンフォーマーの数: 100 / 登録したコンフォーマーの数: 20 / Maximum torsion angle constraint violation: 2.99 ° / Maximum upper distance constraint violation: 0.358 Å