- PDB-4mjg: Crystal structure of a DUF4853 family protein (ACTODO_00621) from... -
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基本情報
登録情報
データベース: PDB / ID: 4mjg
タイトル
Crystal structure of a DUF4853 family protein (ACTODO_00621) from Actinomyces odontolyticus ATCC 17982 at 2.65 A resolution
要素
hypothetical protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF16145 family / DUF4853 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / STRUCTURAL GENOMICS UNKNOWN FUNCTION
機能・相同性
TBP-like - #30 / Protein of unknown function DUF4853 / Domain of unknown function (DUF4853) / TBP-like / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
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 RESIDUES 29-226 OF THE TARGET SEQUENCE.
モノクロメーター: single crystal Si(111) bent / 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
0.91837
1
2
0.97941
1
3
0.97868
1
反射
解像度: 2.65→44.544 Å / Num. all: 15164 / Num. obs: 15164 / % possible obs: 88.9 % / 冗長度: 3.2 % / Rsym value: 0.061 / Net I/σ(I): 9.2
反射 シェル
Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.65-2.72
3.2
0.811
0.9
3833
1182
0.811
95.3
2.72-2.79
3.2
0.531
1.4
3581
1107
0.531
91.4
2.79-2.87
3.1
0.425
1.7
3007
966
0.425
83.5
2.87-2.96
3.2
0.316
2.3
3416
1068
0.316
93.1
2.96-3.06
3.3
0.244
3
3547
1090
0.244
97.1
3.06-3.17
3.3
0.19
3.9
3372
1024
0.19
96.1
3.17-3.29
3.1
0.139
5.3
3092
986
0.139
95.2
3.29-3.42
3.2
0.106
6.7
2930
923
0.106
91.2
3.42-3.57
3.2
0.078
8.9
2504
787
0.078
81.8
3.57-3.75
3.2
0.085
8.5
1845
573
0.085
61.2
3.75-3.95
3.2
0.06
10.8
2062
638
0.06
73.8
3.95-4.19
3.2
0.049
11.9
2603
802
0.049
95.4
4.19-4.48
3.3
0.039
14
2331
711
0.039
90.8
4.48-4.84
3.3
0.036
15.7
1963
601
0.036
81.3
4.84-5.3
3.4
0.04
12.4
2221
660
0.04
96.5
5.3-5.93
3.3
0.04
15.3
1888
579
0.04
94.4
5.93-6.84
3.2
0.037
16.1
1534
478
0.037
85.7
6.84-8.38
3.2
0.033
16.1
1361
432
0.033
90.6
8.38-11.85
3.1
0.032
17.8
1091
357
0.032
94.6
11.85-44.544
2.8
0.042
10.5
570
200
0.042
86.4
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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
MolProbity
3beta29
モデル構築
PDB_EXTRACT
3.1
データ抽出
SHELX
位相決定
SHARP
位相決定
SCALA
3.3.20
データスケーリング
REFMAC
5.7.0032
精密化
MOSFLM
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: 2.65→44.544 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 27.395 / SU ML: 0.262 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.589 / ESU R Free: 0.32 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. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. CHLORIDE (CL),SULFATE (SO4) AND GLYCEROL (GOL) MOLECULES FROM THE PURIFICATION/CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 7. DUE TO STRONG ICE RINGS, REFLECTIONS WERE OMITTED IN THE 3.91-3.86 AND 3.70-3.64 RESOLUTION SHELLS LOWERING THE OVERALL COMPLETENESS TO 88.7%. THE NOMINAL RESOLUTION OF THE RESULTING DATASET IS 2.80 A WITH 2358 OBSERVED REFLECTIONS BETWEEN 2.80-2.65 (92.4% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
Rfactor
反射数
%反射
Selection details
Rfree
0.2609
768
5.1 %
RANDOM
Rwork
0.2336
-
-
-
obs
0.2351
15135
88.7 %
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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: BABINET MODEL WITH MASK