分子量: 7805.653 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Vibrio parahaemolyticus (腸炎ビブリオ) 株: RIMD 2210633 解説: The protein is a monomer by gel filtration chromatography and static light scattering. 遺伝子: VP1593 / プラスミド: VpR55-21.4 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)+Magic / 参照: UniProt: Q87PC4
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実験情報
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実験
実験
手法: 溶液NMR
NMR実験
Conditions-ID
Experiment-ID
Solution-ID
タイプ
1
1
1
2D 1H-15N HSQC
1
2
1
2D 1H-13C HSQC
1
3
1
3D 1H-15N NOESY
1
4
1
3D 1H-13C NOESY
1
5
1
3D 1H-13C NOESY aromatic
1
6
1
3D HNCO
1
7
1
3D HN(CA)CB
1
8
1
3DCBCA(CO)NH
1
9
1
3DHBHA(CO)NH
1
10
1
3DC(CO)NH
1
11
1
3D (H)CCH-TOCSY
1
12
1
3D CCH-TOCSY
1
13
2
2D 1H-13C HSQC high resolution
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試料調製
詳細
Solution-ID
内容
溶媒系
1
1.1 mM [U-100% 13C; U-100% 15N] VpR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O
95% H2O/5% D2O
2
1.1 mM [U-5% 13C; U-100% 15N] VpR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O
95% H2O/5% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
1.1mM
VpR55
[U-100% 13C; U-100% 15N]
1
20mM
MES
naturalabundance
1
100mM
NaCl
naturalabundance
1
5mM
CaCl2
naturalabundance
1
10mM
DTT
naturalabundance
1
0.02 %
NaN3
naturalabundance
1
1.1mM
VpR55
[U-5% 13C; U-100% 15N]
2
20mM
MES
naturalabundance
2
100mM
NaCl
naturalabundance
2
5mM
CaCl2
naturalabundance
2
10mM
DTT
naturalabundance
2
0.02 %
NaN3
naturalabundance
2
試料状態
イオン強度: 100 / pH: 6.5 / 圧: ambient / 温度: 293 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
Bruker Avance
Bruker
AVANCE
800
1
Bruker Avance
Bruker
AVANCE
600
2
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解析
NMR software
名称
バージョン
開発者
分類
TopSpin
1.3
BrukerBiospin
collection
AutoAssign
2.2.1
Zimmerman, Moseley, KulikowskiandMontelione
chemicalshiftassignment
Sparky
3.11
Goddard
peakpicking
Sparky
3.11
Goddard
データ解析
AutoStructure
2.1.1
Huang, Tejero, PowersandMontelione
構造決定
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
解析
X-PLOR NIH
2.11.2
Schwieters, Kuszewski, TjandraandClore
構造決定
X-PLOR NIH
2.11.2
Schwieters, Kuszewski, TjandraandClore
精密化
CNS
1.1
Brunger, Adams, Clore, Gros, NilgesandRead
構造決定
CNS
1.1
Brunger, Adams, Clore, Gros, NilgesandRead
精密化
PSVS
1.3
BhattacharyaandMontelione
データ解析
PdbStat
4
TejeroandMontelione
pdbanalysis
CYANA
Guntert, MumenthalerandWuthrich
構造決定
精密化
手法: simulated annealing / ソフトェア番号: 10 詳細: THE STRUCTURES ARE BASED ON A TOTAL OF 865 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 154 DIHEDRAL ANGLE CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (18.4 CONSTRAINTS ...詳細: THE STRUCTURES ARE BASED ON A TOTAL OF 865 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 154 DIHEDRAL ANGLE CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (18.4 CONSTRAINTS PER RESIDUE, 2.8 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 60 BY PSVS 1.3) STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE. THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE C-TERMINAL HIS TAG RESDIUES OF THE PROTEIN (HHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED(S(PHI)+S(PSI)<1.8): 1-4, 54-60. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN ASSIGNMENTS WERE CO PLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, HIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENT (EXCLUDING C-TERMINAL HHHHH): BACKBONE,99.66%, SIDE CHAIN, 92.20%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-60 PSVS 1.3), WHERE ORDERED RESIDUES (S(PHI)+S(PSI)>1.8) COMPRISE: 5-54. (A) RMSD (ORDERED RESIDUES): BB 0.5, HEAVY ATOM: 1.2 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 83.6%, ADDITIONALLY ALLOWED: 13.8%, GENEROUSLY ALLOWED : 0.2%, DISALLOWED,2.3%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.14/-0.24, ALL , -0.16/-0.95. (D) MOLPROBITY CLASH SCORE (RAW/Z): 19.25/-1.78. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-60): RECALL, 0.962, PRECISION, 0.921, F-MEASURE, 0.941, DP-SCORE, 0.804.
NMR constraints
NOE constraints total: 865 / NOE intraresidue total count: 171 / NOE long range total count: 164 / NOE medium range total count: 277 / NOE sequential total count: 253
代表構造
選択基準: lowest energy
NMRアンサンブル
コンフォーマー選択の基準: structures with the lowest energy 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: 4.9 ° / Maximum upper distance constraint violation: 0.45 Å