- PDB-3o0r: Crystal structure of nitric oxide reductase from Pseudomonas aeru... -
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基本情報
登録情報
データベース: PDB / ID: 3o0r
タイトル
Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment
要素
(Nitric oxide reductase subunit ...) x 2
(antibody fab fragment ...) x 2
キーワード
IMMUNE SYSTEM/OXIDOREDUCTASE / oxidoreductase / electron transport / heme / iron / membrane / cytoplasmic membrane / IMMUNE SYSTEM-OXIDOREDUCTASE complex
機能・相同性
機能・相同性情報
nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / denitrification pathway / cytochrome-c oxidase activity / aerobic respiration / respiratory electron transport chain / electron transfer activity / heme binding / metal ion binding / plasma membrane 類似検索 - 分子機能
: / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I ...: / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha 類似検索 - ドメイン・相同性
: / HEME C / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Nitric oxide reductase subunit C / Nitric oxide reductase subunit B 類似検索 - 構成要素
#232 - 2019年4月 タンパク質と生体鉱物 (Proteins and Biominerals) 類似性 (1)
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集合体
登録構造単位
L: antibody fab fragment light chain H: antibody fab fragment heavy chain B: Nitric oxide reductase subunit B C: Nitric oxide reductase subunit C ヘテロ分子
冗長度: 11.9 % / Av σ(I) over netI: 5.65 / 数: 530738 / Rmerge(I) obs: 0.101 / Rsym value: 0.094 / Χ2: 2.31 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 44758 / % possible obs: 96.8
Diffraction reflection shell
ID: 1
最高解像度 (Å)
最低解像度 (Å)
% possible obs (%)
Rmerge(I) obs
Rsym value
Chi squared
Redundancy
7.59
50
96.2
0.039
0.034
2.732
12.7
6.03
7.59
100
0.057
0.044
2.646
13.9
5.27
6.03
100
0.072
0.111
2.945
13
4.79
5.27
99.7
0.072
0.075
2.964
12.7
4.44
4.79
99.4
0.074
0.074
2.743
12.6
4.18
4.44
99.9
0.083
0.117
2.48
12.6
3.97
4.18
99.6
0.101
0.184
2.332
12.6
3.8
3.97
99.6
0.137
0.316
2.25
12.7
3.65
3.8
99.8
0.17
0.489
1.897
12.6
3.53
3.65
99.5
0.195
0.786
2.006
12.7
3.42
3.53
99.5
0.251
2.048
12.6
3.32
3.42
99.6
0.306
2.089
12.6
3.23
3.32
99.4
0.395
2.307
12.3
3.15
3.23
99.2
0.442
1.905
11.8
3.08
3.15
98.5
0.499
2.486
11
3.02
3.08
97.2
0.577
2.035
10.4
2.96
3.02
93.7
0.559
1.795
9.9
2.9
2.96
89.4
0.565
1.843
9.4
2.85
2.9
84.7
0.667
1.711
8.9
2.8
2.85
81.4
0.634
1.968
8.1
反射
解像度: 2.7→41.514 Å / Num. all: 50332 / Num. obs: 50332 / % possible obs: 97.7 % / 冗長度: 4.2 % / Rsym value: 0.094 / Net I/σ(I): 8.3
反射 シェル
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Rsym value
Diffraction-ID
% possible all
2.7-2.85
4.2
0.786
1
0.786
1,2,3
99
2.85-3.02
4.2
0.489
1.5
0.489
1,2,3
98.8
3.02-3.23
4.2
0.316
2.4
0.316
1,2,3
98.7
3.23-3.49
4.2
0.184
3.9
0.184
1,2,3
98.2
3.49-3.82
4.2
0.117
6
0.117
1,2,3
98.2
3.82-4.27
4.2
0.074
8.7
0.074
1,2,3
97.7
4.27-4.93
4.2
0.075
7.6
0.075
1,2,3
97.2
4.93-6.04
4.2
0.111
5.3
0.111
1,2,3
96.7
6.04-8.54
4.2
0.044
13
0.044
1,2,3
95.8
8.54-41.514
3.8
0.034
17.8
0.034
1,2,3
87.1
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位相決定
位相決定
手法: 分子置換
Phasing MR
Rfactor: 56.55 / Model details: Phaser MODE: MR_RNP
Phasing dm
手法: Solvent flattening and Histogram matching / 反射: 44644
Phasing dm shell
解像度 (Å)
Delta phi final
FOM
反射
12.52-100
60.5
0.532
514
9.66-12.52
58.8
0.79
652
8.15-9.66
60.4
0.777
782
7.18-8.15
63.9
0.802
913
6.49-7.18
64.9
0.777
990
5.97-6.49
69.3
0.762
1095
5.55-5.97
69.6
0.78
1173
5.21-5.55
64.6
0.815
1254
4.93-5.21
69.7
0.826
1305
4.69-4.93
67.5
0.827
1388
4.48-4.69
66.1
0.851
1443
4.3-4.48
66
0.861
1521
4.14-4.3
68.5
0.845
1560
3.99-4.14
68.4
0.828
1618
3.86-3.99
66.4
0.834
1673
3.74-3.86
72.5
0.826
1728
3.63-3.74
70.6
0.843
1780
3.53-3.63
72.7
0.848
1838
3.44-3.53
75.5
0.841
1886
3.35-3.44
74.8
0.852
1913
3.28-3.35
75.3
0.835
1974
3.2-3.28
76.1
0.821
2008
3.13-3.2
79.8
0.811
2019
3.07-3.13
78.3
0.784
2075
3.01-3.07
80.8
0.776
2088
2.95-3.01
82.7
0.762
2024
2.9-2.95
81.4
0.753
1964
2.8-2.9
82.4
0.619
3466
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解析
ソフトウェア
名称
バージョン
分類
NB
MOSFLM
データ削減
SCALA
3.3.16
データスケーリング
PHASER
2.1.4
位相決定
直接法
6.1
位相決定
REFMAC
精密化
PDB_EXTRACT
3.1
データ抽出
精密化
構造決定の手法: 分子置換 / 解像度: 2.7→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.773 / SU ML: 0.241 / SU R Cruickshank DPI: 0.3943 / 交差検証法: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.287 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.24739
2559
5.1 %
RANDOM
Rwork
0.18523
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obs
0.18828
47669
97.49 %
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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: 1.4 Å / 溶媒モデル: MASK