- PDB-3d00: Crystal structure of a tungsten formylmethanofuran dehydrogenase ... -
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基本情報
登録情報
データベース: PDB / ID: 3d00
タイトル
Crystal structure of a tungsten formylmethanofuran dehydrogenase subunit e (fmde)-like protein (syn_00638) from syntrophus aciditrophicus at 1.90 A resolution
要素
Tungsten formylmethanofuran dehydrogenase subunit E
キーワード
METAL BINDING PROTEIN / Fwde/gapdh domain-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
AUTHORS STATE THAT THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT 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 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
0.91837
1
2
0.97817
1
反射
解像度: 1.9→29.386 Å / Num. obs: 16955 / % possible obs: 99.9 % / 冗長度: 7 % / Biso Wilson estimate: 30.675 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 6.8
反射 シェル
Rmerge(I) obs: 0.011 / Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.9-1.95
7.1
0.7
8626
1208
1.134
99.9
1.95-2
7.2
0.9
8582
1192
0.855
99.9
2-2.06
7.1
1.2
8253
1157
0.659
100
2.06-2.12
7.1
1.6
8020
1122
0.484
100
2.12-2.19
7.2
1.9
7887
1102
0.41
100
2.19-2.27
7.1
2.3
7549
1068
0.34
100
2.27-2.36
7.2
2.8
7325
1018
0.281
100
2.36-2.45
7.1
3.3
7032
989
0.235
100
2.45-2.56
7.1
4.2
6743
953
0.185
100
2.56-2.69
7.1
5.1
6522
920
0.148
100
2.69-2.83
7
6.1
6142
872
0.122
100
2.83-3
7
7.3
5834
837
0.097
100
3-3.21
7
8.6
5569
796
0.079
100
3.21-3.47
7
10.5
5024
718
0.062
100
3.47-3.8
6.9
13.2
4748
693
0.049
100
3.8-4.25
6.8
13.6
4272
631
0.044
100
4.25-4.91
6.7
14.8
3748
561
0.041
100
4.91-6.01
6.5
16
3173
485
0.041
100
6.01-8.5
6
14.3
2353
394
0.041
100
8.5-29.386
5.2
16.4
1244
239
0.035
95.9
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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
SCALA
データスケーリング
PDB_EXTRACT
3.004
データ抽出
MAR345
CCD
データ収集
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: 1.9→29.386 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.433 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.156 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ZINC WAS MODELED BASED ON X-RAY FLUORESCENCE SCAN AND ANOMALOUS DIFFERENCE FOURIER MAP CALCULATIONS. 5. CHLORIDE WAS MODELED BASED ON CRYSTALLIZATION CONDITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.268
855
5.1 %
RANDOM
Rwork
0.233
-
-
-
obs
0.235
16902
99.9 %
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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
原子変位パラメータ
Biso mean: 35.2 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.73 Å2
0 Å2
0 Å2
2-
-
1.73 Å2
0 Å2
3-
-
-
-3.46 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.9→29.386 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1388
0
2
42
1432
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.022
1445
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
961
X-RAY DIFFRACTION
r_angle_refined_deg
1.604
1.987
1972
X-RAY DIFFRACTION
r_angle_other_deg
1.031
3
2356
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.4
5
189
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.474
23.774
53
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.661
15
225
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.608
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
224
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1615
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
292
X-RAY DIFFRACTION
r_nbd_refined
0.2
0.2
285
X-RAY DIFFRACTION
r_nbd_other
0.196
0.2
900
X-RAY DIFFRACTION
r_nbtor_refined
0.182
0.2
710
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
747
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.175
0.2
37
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.114
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.226
0.2
37
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.178
0.2
15
X-RAY DIFFRACTION
r_mcbond_it
1.214
2
954
X-RAY DIFFRACTION
r_mcbond_other
0.264
2
376
X-RAY DIFFRACTION
r_mcangle_it
1.913
3
1489
X-RAY DIFFRACTION
r_scbond_it
1.086
2
576
X-RAY DIFFRACTION
r_scangle_it
1.576
3
480
LS精密化 シェル
解像度: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.351
64
-
Rwork
0.347
1136
-
all
-
1200
-
obs
-
-
99.75 %
精密化 TLS
手法: refined / Origin x: 16.6441 Å / Origin y: 25.3781 Å / Origin z: 61.974 Å