- PDB-3t0p: Crystal structure of a Putative DNA polymerase III beta subunit (... -
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基本情報
登録情報
データベース: PDB / ID: 3t0p
タイトル
Crystal structure of a Putative DNA polymerase III beta subunit (EUBREC_0002; ERE_29750) from Eubacterium rectale ATCC 33656 at 2.26 A resolution
要素
DNA polymerase III, beta subunit
キーワード
TRANSFERASE / DNA clamp / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
機能・相同性
機能・相同性情報
DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm 類似検索 - 分子機能
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / Roll / Alpha Beta 類似検索 - ドメイン・相同性
CRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS THE STABLE OLIGOMERIC FORM IN SOLUTION.
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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.
解像度: 2.26→29.632 Å / Num. obs: 41878 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.182 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.62
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
2.26-2.34
0.578
1.8
16816
8062
1
95.6
2.34-2.43
0.468
2.3
16020
7679
1
96.2
2.43-2.54
0.377
3
16960
8121
1
96.4
2.54-2.68
0.276
4.1
17536
8403
1
95.9
2.68-2.85
0.201
5.6
17033
8165
1
96.1
2.85-3.07
0.12
8.5
16695
8023
1
95.7
3.07-3.37
0.066
13.1
15826
7658
1
93.7
3.37-3.86
0.036
19.6
15449
7561
1
89.6
3.86-4.85
0.023
28.7
15107
7446
1
89.4
4.85-29.632
0.02
32.4
15355
7660
1
89.7
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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
XSCALE
December6, 2010
データスケーリング
BUSTER-TNT
2.8.0
精密化
XDS
データ削減
SHELXD
位相決定
BUSTER
2.8.0
精密化
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.26→29.632 Å / Cor.coef. Fo:Fc: 0.9528 / Cor.coef. Fo:Fc free: 0.9316 / Occupancy max: 1 / Occupancy min: 0.25 / 交差検証法: THROUGHOUT / σ(F): 0 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. 1,2 ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT AND ACETATE (ACT), R-1,2-PROPANEDIOL (PGR) AND CHLORIDE ION (CL) FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).