- PDB-2hkv: CRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1... -
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基本情報
登録情報
データベース: PDB / ID: 2hkv
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1237) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.70 A RESOLUTION
要素
Hypothetical protein
キーワード
DNA BINDING PROTEIN / PUTATIVE MEMBER OF THE DINB FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
機能・相同性
機能・相同性情報
DNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha 類似検索 - ドメイン・相同性
NICKEL (II) ION / Uncharacterized protein / : 類似検索 - 構成要素
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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.
20.0% PEG-3350, 0.2M MgSO4,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
293
2
蒸気拡散法, シッティングドロップ法, nanodrop
20.0% PEG-3350, 0.2M MgSO4,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
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データ収集
回折
ID
平均測定温度 (K)
Crystal-ID
1
100
1
2
100
2
放射光源
由来
サイト
ビームライン
ID
波長 (Å)
シンクロトロン
SSRL
BL9-2
1
0.97925
シンクロトロン
SSRL
BL9-2
2
0.92522, 0.97934
検出器
タイプ
ID
検出器
日付
詳細
MARMOSAIC 325 mm CCD
1
CCD
2006年6月17日
Flatcollimatingmirror, toroidfocusingmirror
MARMOSAIC 325 mm CCD
2
CCD
2006年6月17日
Flatcollimatingmirror, toroidfocusingmirror
放射
ID
モノクロメーター
プロトコル
単色(M)・ラウエ(L)
散乱光タイプ
Wavelength-ID
1
Doublecrystalmonochromator
SINGLEWAVELENGTH
M
x-ray
1
2
Doublecrystalmonochromator
MAD
M
x-ray
2
放射波長
ID
波長 (Å)
相対比
1
0.97925
1
2
0.92522
1
3
0.97934
1
反射
解像度: 1.7→25.094 Å / Num. obs: 17704 / % possible obs: 99.8 % / 冗長度: 9.38 % / Biso Wilson estimate: 37.034 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.58
反射 シェル
Diffraction-ID: 1,2
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique all
% possible all
1.7-1.76
7.01
0.97
1.99
10939
1533
99.8
1.76-1.83
0.732
2.8
11534
1600
92.5
1.83-1.91
0.571
3.4
11264
1565
93.5
1.91-2.02
0.375
5.2
13211
1849
97
2.02-2.14
0.262
7
11687
1643
98.6
2.14-2.31
0.226
10.1
18428
1781
99.4
2.31-2.54
0.187
12.9
21841
1748
99.8
2.54-2.9
0.152
14.6
21615
1752
99.9
2.9-25.1
0.115
17
22091
1825
100
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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
REFMAC
5.2.0019
精密化
XSCALE
データスケーリング
PDB_EXTRACT
2
データ抽出
SOLVE
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.7→25.094 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.318 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.111 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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE ASSIGNMENT OF THE METAL AS PREDOMINATELY NICKEL IS BASED ON BOTH X-RAY FLUORECENCE METAL SCAN AND DIFFERENCE MAPS (ABOVE AND BELOW NICKEL AND ZINC EDGES). 5. THE ASSIGNMENT OF CHLORIDES ARE BASED ON DIFFERENCE DENSITY. 6. THE DISORDER ON TWO-FOLD BY RESIDUE 4 INDICATED THAT THE SPACE GROUP IS NOT STRICTLY P3221 BUT P32, REFINEMENT IN P3221 RESULTS ONLY ~1% INCREASE IN RFACTOR AND RFREE COMPARED TO P32, THUS THE SPACE GROUP WAS ASSIGNED AS HIGHER SYMMETRY P3221. 7. THE EXPERIMENTAL PHASES ARE FROM A DIFFERENT CRYSTAL, THEY ARE USED AS RESTRAINTS IN REFINEMENT. 8. DENSITY FOR RESIDUE 99 IS POOR.
Rfactor
反射数
%反射
Selection details
Rfree
0.227
1361
7.7 %
RANDOM
Rwork
0.181
-
-
-
all
0.185
-
-
-
obs
0.18514
17699
99.86 %
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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
原子変位パラメータ
Biso mean: 33.948 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.63 Å2
-0.32 Å2
0 Å2
2-
-
-0.63 Å2
0 Å2
3-
-
-
0.95 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.7→25.094 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1197
0
4
65
1266
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
1245
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
810
X-RAY DIFFRACTION
r_angle_refined_deg
1.451
1.935
1704
X-RAY DIFFRACTION
r_angle_other_deg
1.025
3
1960
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.273
5
151
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
28.465
23.115
61
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.219
15
199
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.044
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
192
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1388
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
272
X-RAY DIFFRACTION
r_nbd_refined
0.223
0.2
305
X-RAY DIFFRACTION
r_nbd_other
0.179
0.2
812
X-RAY DIFFRACTION
r_nbtor_refined
0.191
0.2
615
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.2
587
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.176
0.2
42
X-RAY DIFFRACTION
r_metal_ion_refined
0.401
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.292
0.2
6
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.302
0.2
24
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.092
0.2
4
X-RAY DIFFRACTION
r_mcbond_it
2.642
3
815
X-RAY DIFFRACTION
r_mcbond_other
0.607
3
301
X-RAY DIFFRACTION
r_mcangle_it
3.507
5
1197
X-RAY DIFFRACTION
r_scbond_it
5.706
8
581
X-RAY DIFFRACTION
r_scangle_it
7.64
11
505
LS精密化 シェル
解像度: 1.7→1.744 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.34
99
-
Rwork
0.269
1168
-
obs
-
1267
99.69 %
精密化 TLS
手法: refined / Origin x: 7.135 Å / Origin y: -0.881 Å / Origin z: -8.439 Å