- PDB-2p4o: CRYSTAL STRUCTURE OF A PUTATIVE LACTONASE OF THE SMP-30/GLUCONOLA... -
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データベース: PDB / ID: 2p4o
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE LACTONASE OF THE SMP-30/GLUCONOLACTONASE/LRE-LIKE REGION FAMILY (NPUN_F0524) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.90 A RESOLUTION
要素
hypothetical protein
キーワード
HYDROLASE / PUTATIVE LACTONASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. 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. 2. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. 3. THE SEQUENCE IS AVAILABLE FROM GENBANK UNDER ACCESSION ID ZP_00111901.1 AND FROM THE UNIPROT ARCHIVE UNDER ACCESSION ID UPI000038C6E7.
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
0.97895
1
3
0.97925
1
反射
解像度: 1.9→29.696 Å / Num. obs: 25746 / % possible obs: 100 % / 冗長度: 7.1 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 6
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
1.9-1.95
7.2
0.752
1
13433
1865
0.752
100
1.95-2
7.3
0.558
1.4
13327
1828
0.558
100
2-2.06
7.3
0.442
1.8
12793
1757
0.442
100
2.06-2.12
7.2
0.329
2.3
12427
1725
0.329
100
2.12-2.19
7.3
0.262
3
12221
1678
0.262
100
2.19-2.27
7.2
0.231
3.3
11769
1627
0.231
100
2.27-2.36
7.3
0.179
4.3
11239
1549
0.179
100
2.36-2.45
7.3
0.157
4.8
11057
1521
0.157
100
2.45-2.56
7.2
0.139
5.2
10511
1452
0.139
100
2.56-2.69
7.2
0.119
5.9
10126
1402
0.119
100
2.69-2.83
7.2
0.098
7
9518
1318
0.098
100
2.83-3
7.2
0.085
7.6
9059
1256
0.085
100
3-3.21
7.1
0.079
7.8
8477
1191
0.079
100
3.21-3.47
7.1
0.074
8.2
7912
1121
0.074
100
3.47-3.8
7.1
0.065
9.3
7260
1029
0.065
100
3.8-4.25
7
0.053
11.5
6502
935
0.053
100
4.25-4.91
6.9
0.048
12.5
5810
848
0.048
100
4.91-6.01
6.8
0.047
12.4
4880
722
0.047
100
6.01-8.5
6.5
0.041
14.8
3777
583
0.041
100
8.5-29.7
5.7
0.037
16.2
1931
339
0.037
97
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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
SOLVE
位相決定
REFMAC
5.2.0005
精密化
SCALA
データスケーリング
PDB_EXTRACT
2
データ抽出
MAR345
CCD
データ収集
MOSFLM
データ削減
CCP4
(SCALA)
データスケーリング
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.9→29.696 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.068 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.133 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. GOL IS MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. ACT IS MODELED IN THE PUTATIVE ACTIVE SITE. 6. RAMACHANDRAN OUTLIER ASP 214 IS SUPPORTED BY DENSITY.
Rfactor
反射数
%反射
Selection details
Rfree
0.219
1307
5.1 %
RANDOM
Rwork
0.172
-
-
-
all
0.174
-
-
-
obs
0.174
25661
99.97 %
-
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: 39.328 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.1 Å2
0 Å2
0 Å2
2-
-
0.1 Å2
0 Å2
3-
-
-
-0.21 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.9→29.696 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2246
0
10
134
2390
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
2336
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2146
X-RAY DIFFRACTION
r_angle_refined_deg
1.591
1.974
3209
X-RAY DIFFRACTION
r_angle_other_deg
0.866
3
4996
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.273
5
311
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.546
25.227
88
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.913
15
345
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.635
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
384
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2629
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
431
X-RAY DIFFRACTION
r_nbd_refined
0.211
0.2
387
X-RAY DIFFRACTION
r_nbd_other
0.185
0.2
2196
X-RAY DIFFRACTION
r_nbtor_refined
0.172
0.2
1146
X-RAY DIFFRACTION
r_nbtor_other
0.086
0.2
1394
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.159
0.2
134
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.598
0.2
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.16
0.2
33
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.314
0.2
5
X-RAY DIFFRACTION
r_mcbond_it
2.15
3
1612
X-RAY DIFFRACTION
r_mcbond_other
0.55
3
615
X-RAY DIFFRACTION
r_mcangle_it
3.061
5
2484
X-RAY DIFFRACTION
r_scbond_it
5.492
8
883
X-RAY DIFFRACTION
r_scangle_it
7.002
11
720
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
0.294
99
-
Rwork
0.219
1713
-
obs
-
1812
100 %
精密化 TLS
手法: refined / Origin x: 22.388 Å / Origin y: 31.339 Å / Origin z: 19.633 Å