IN CONTRAST WITH THE PREVIOUSLY DEPOSITED IN PDB STRUCTURES OF EQUUS CABALLUS SA (PDB IDS: 3V08, ...IN CONTRAST WITH THE PREVIOUSLY DEPOSITED IN PDB STRUCTURES OF EQUUS CABALLUS SA (PDB IDS: 3V08, 4J2V, 4OT2, 4F5U, AND 4F5T), A SINGLE POINT MUTATION, R561A, IS OBSERVED. THE LONG ARGININE SIDE CHAIN CANNOT BE MODELED IN THIS POSITION DUE TO STERIC CLASHES WITH THE NEARBY DISULFIDE BOND CONNECTING CYS567 AND CYS558 AND A SYMMETRY-COPY OF THE MOLECULE. MOREOVER, THERE IS NO 2MFO-DFC OMIT MAP SUPPORTING PLACEMENT OF THE SIDE CHAIN. PROTEIN WAS PURIFIED FROM NATURAL SOURCE, THEREFORE THERE MAY BE NATURALLY OCCURRING MUTATION. ACCORDING TO THE NCBI DATABASE, THIS MUTATION IS CHARACTERISTIC FOR EQUUS FERUS PRZEWALSKII, A RARE SUBSPECIES OF WILD HORSE FROM CENTRAL ASIA (ACCESSION CODE: XP_008524663.1). HOWEVER IT IS POSSIBLE THAT THERE IS AN ERROR IN THE EQUUS CABALLUS SA SEQUENCE, OR THE OBSERVED MUTATION NATURALLY OCCURS IN THAT SPECIES.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 2.77 Å3/Da / 溶媒含有率: 55.67 % 解説: The author states that two data sets were collected on the same crystal in order to prove the entity and position of metal in the structure. The first data set was collected on the wavelength ...解説: The author states that two data sets were collected on the same crystal in order to prove the entity and position of metal in the structure. The first data set was collected on the wavelength above zinc absorption edge and the second below zinc absorption edge.
結晶化
温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.4 詳細: 1 ul of 30 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.0 M (NH4)2SO4, 5 mM ZnCl2, final pH 7.4) and ...詳細: 1 ul of 30 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.0 M (NH4)2SO4, 5 mM ZnCl2, final pH 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 100 mM ZnCl2 in 100 mM Tris, final pH 7.4, to final concentration of 100 mM
解像度: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2426 / WRfactor Rwork: 0.184 / FOM work R set: 0.7597 / SU B: 20.243 / SU ML: 0.244 / SU R Cruickshank DPI: 0.3854 / SU Rfree: 0.2654 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.265 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.2553
1418
5.1 %
RANDOM
Rwork
0.1954
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obs
0.1985
26459
99.56 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK