- PDB-3fm2: CRYSTAL STRUCTURE OF A PUTATIVE HEME-BINDING PROTEIN (AVA_4353) F... -
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基本情報
登録情報
データベース: PDB / ID: 3fm2
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE HEME-BINDING PROTEIN (AVA_4353) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.80 A RESOLUTION
要素
Uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family
キーワード
HEME-BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
機能・相同性
Intracellular heme transport protein HutX-like / Haem utilisation ChuX/HutX / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / ACETATE ION / Uncharacterized protein
ジャーナル: To be published タイトル: Crystal structure of uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family (YP_324846.1) from Anabaena variabilis ATCC 29413 at 1.80 A resolution 著者: Joint Center for Structural Genomics (JCSG)
A: Uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family B: Uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family ヘテロ分子
CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE DIMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION. ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.
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要素
#1: タンパク質
Uncharacterizedprotein, distantlyrelatedtoahemebinding/degradingHemS (PF05171) family
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
モノクロメーター: Single crystal Si(111) bent (horizontal focusing) プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID
波長 (Å)
相対比
1
0.91162
1
2
0.9787
1
3
0.97828
1
反射
解像度: 1.8→29.001 Å / Num. obs: 25482 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / 冗長度: 3.6 % / Biso Wilson estimate: 25.168 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.16
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.8-1.86
0.432
2.03
8422
4421
1
98.8
1.86-1.94
0.29
2.9
9837
5148
1
99.2
1.94-2.03
0.208
3.8
9196
4810
1
99
2.03-2.13
0.141
5.6
8626
4489
1
98.9
2.13-2.27
0.103
7.4
9596
4988
1
99
2.27-2.44
0.081
9.1
9004
4665
1
99.1
2.44-2.69
0.057
12.2
9385
4837
1
99
2.69-3.07
0.038
16.4
9041
4672
1
98.9
3.07-3.87
0.026
23.5
9312
4783
1
98.6
3.87-29.001
0.022
28.9
9226
4709
1
96.9
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位相決定
位相決定
手法: 多波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
3.006
データ抽出
MAR345
CCD
データ収集
XDS
データ削減
SHELXD
位相決定
autoSHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.8→29.001 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.696 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.123 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ACETATE (ACT) FROM THE CRYSTALLIZATION CONDITION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 4. ZINC (ZN) HAS BEEN MODELED IN BOTH PROTEIN MOLECULES BASED ON A FLUORESCENCE SCAN AND ANOMALOUS DIFFERENCE FOURIER MAPS.
Rfactor
反射数
%反射
Selection details
Rfree
0.219
1302
5.1 %
RANDOM
Rwork
0.196
-
-
-
obs
0.197
25437
99.49 %
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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