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- PDB-6ekc: Crystal structure of the BSD2 homolog of Arabidopsis thaliana bou... -

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基本情報

登録情報
データベース: PDB / ID: 6ekc
タイトルCrystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus
要素
  • DnaJ/Hsp40 cysteine-rich domain superfamily protein
  • Ribulose bisphosphate carboxylase large chain
キーワードCHAPERONE / zinc finger / assembly chaperone / assembly intermediate
機能・相同性
機能・相同性情報


ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone ...ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone / monooxygenase activity / chloroplast / magnesium ion binding / metal ion binding / cytoplasm / cytosol
類似検索 - 分子機能
Heat shock protein DnaJ, cysteine-rich domain superfamily / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
類似検索 - ドメイン・相同性
Ribulose bisphosphate carboxylase large chain / Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
類似検索 - 構成要素
生物種Thermosynechococcus elongatus (バクテリア)
Arabidopsis thaliana (シロイヌナズナ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.63 Å
データ登録者Aigner, H. / Wilson, R.H. / Bracher, A. / Calisse, L. / Bhat, J.Y. / Hartl, F.U. / Hayer-Hartl, M.
引用ジャーナル: Science / 年: 2017
タイトル: Plant RuBisCo assembly in E. coli with five chloroplast chaperones including BSD2.
著者: Aigner, H. / Wilson, R.H. / Bracher, A. / Calisse, L. / Bhat, J.Y. / Hartl, F.U. / Hayer-Hartl, M.
履歴
登録2017年9月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年12月6日Provider: repository / タイプ: Initial release
改定 1.12017年12月20日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22018年1月24日Group: Source and taxonomy / カテゴリ: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
改定 1.32024年1月17日Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A1: Ribulose bisphosphate carboxylase large chain
A2: Ribulose bisphosphate carboxylase large chain
A3: Ribulose bisphosphate carboxylase large chain
A4: Ribulose bisphosphate carboxylase large chain
A5: Ribulose bisphosphate carboxylase large chain
A6: Ribulose bisphosphate carboxylase large chain
A7: Ribulose bisphosphate carboxylase large chain
A8: Ribulose bisphosphate carboxylase large chain
C1: Ribulose bisphosphate carboxylase large chain
C2: Ribulose bisphosphate carboxylase large chain
C3: Ribulose bisphosphate carboxylase large chain
C4: Ribulose bisphosphate carboxylase large chain
C5: Ribulose bisphosphate carboxylase large chain
C6: Ribulose bisphosphate carboxylase large chain
C7: Ribulose bisphosphate carboxylase large chain
C8: Ribulose bisphosphate carboxylase large chain
E1: Ribulose bisphosphate carboxylase large chain
E2: Ribulose bisphosphate carboxylase large chain
E3: Ribulose bisphosphate carboxylase large chain
E4: Ribulose bisphosphate carboxylase large chain
E5: Ribulose bisphosphate carboxylase large chain
E6: Ribulose bisphosphate carboxylase large chain
E7: Ribulose bisphosphate carboxylase large chain
E8: Ribulose bisphosphate carboxylase large chain
G1: Ribulose bisphosphate carboxylase large chain
G2: Ribulose bisphosphate carboxylase large chain
G3: Ribulose bisphosphate carboxylase large chain
G4: Ribulose bisphosphate carboxylase large chain
G5: Ribulose bisphosphate carboxylase large chain
G6: Ribulose bisphosphate carboxylase large chain
G7: Ribulose bisphosphate carboxylase large chain
G8: Ribulose bisphosphate carboxylase large chain
I1: Ribulose bisphosphate carboxylase large chain
I2: Ribulose bisphosphate carboxylase large chain
I3: Ribulose bisphosphate carboxylase large chain
I4: Ribulose bisphosphate carboxylase large chain
I5: Ribulose bisphosphate carboxylase large chain
I6: Ribulose bisphosphate carboxylase large chain
I7: Ribulose bisphosphate carboxylase large chain
I8: Ribulose bisphosphate carboxylase large chain
K1: Ribulose bisphosphate carboxylase large chain
K2: Ribulose bisphosphate carboxylase large chain
K3: Ribulose bisphosphate carboxylase large chain
K4: Ribulose bisphosphate carboxylase large chain
K5: Ribulose bisphosphate carboxylase large chain
K6: Ribulose bisphosphate carboxylase large chain
K7: Ribulose bisphosphate carboxylase large chain
K8: Ribulose bisphosphate carboxylase large chain
M1: Ribulose bisphosphate carboxylase large chain
M2: Ribulose bisphosphate carboxylase large chain
M3: Ribulose bisphosphate carboxylase large chain
M4: Ribulose bisphosphate carboxylase large chain
M5: Ribulose bisphosphate carboxylase large chain
M6: Ribulose bisphosphate carboxylase large chain
M7: Ribulose bisphosphate carboxylase large chain
M8: Ribulose bisphosphate carboxylase large chain
O1: Ribulose bisphosphate carboxylase large chain
O2: Ribulose bisphosphate carboxylase large chain
O3: Ribulose bisphosphate carboxylase large chain
O4: Ribulose bisphosphate carboxylase large chain
O5: Ribulose bisphosphate carboxylase large chain
O6: Ribulose bisphosphate carboxylase large chain
O7: Ribulose bisphosphate carboxylase large chain
O8: Ribulose bisphosphate carboxylase large chain
Q1: Ribulose bisphosphate carboxylase large chain
Q2: Ribulose bisphosphate carboxylase large chain
Q3: Ribulose bisphosphate carboxylase large chain
Q4: Ribulose bisphosphate carboxylase large chain
Q5: Ribulose bisphosphate carboxylase large chain
Q6: Ribulose bisphosphate carboxylase large chain
Q7: Ribulose bisphosphate carboxylase large chain
Q8: Ribulose bisphosphate carboxylase large chain
S1: Ribulose bisphosphate carboxylase large chain
S2: Ribulose bisphosphate carboxylase large chain
S3: Ribulose bisphosphate carboxylase large chain
S4: Ribulose bisphosphate carboxylase large chain
S5: Ribulose bisphosphate carboxylase large chain
S6: Ribulose bisphosphate carboxylase large chain
S7: Ribulose bisphosphate carboxylase large chain
S8: Ribulose bisphosphate carboxylase large chain
B1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)4,921,405320
ポリマ－4,910,939160
非ポリマー10,465160
水11,043613
1
A1: Ribulose bisphosphate carboxylase large chain
A2: Ribulose bisphosphate carboxylase large chain
A3: Ribulose bisphosphate carboxylase large chain
A4: Ribulose bisphosphate carboxylase large chain
A5: Ribulose bisphosphate carboxylase large chain
A6: Ribulose bisphosphate carboxylase large chain
A7: Ribulose bisphosphate carboxylase large chain
A8: Ribulose bisphosphate carboxylase large chain
B1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水19811
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C1: Ribulose bisphosphate carboxylase large chain
C2: Ribulose bisphosphate carboxylase large chain
C3: Ribulose bisphosphate carboxylase large chain
C4: Ribulose bisphosphate carboxylase large chain
C5: Ribulose bisphosphate carboxylase large chain
C6: Ribulose bisphosphate carboxylase large chain
C7: Ribulose bisphosphate carboxylase large chain
C8: Ribulose bisphosphate carboxylase large chain
D1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水21612
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E1: Ribulose bisphosphate carboxylase large chain
E2: Ribulose bisphosphate carboxylase large chain
E3: Ribulose bisphosphate carboxylase large chain
E4: Ribulose bisphosphate carboxylase large chain
E5: Ribulose bisphosphate carboxylase large chain
E6: Ribulose bisphosphate carboxylase large chain
E7: Ribulose bisphosphate carboxylase large chain
E8: Ribulose bisphosphate carboxylase large chain
F1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G1: Ribulose bisphosphate carboxylase large chain
G2: Ribulose bisphosphate carboxylase large chain
G3: Ribulose bisphosphate carboxylase large chain
G4: Ribulose bisphosphate carboxylase large chain
G5: Ribulose bisphosphate carboxylase large chain
G6: Ribulose bisphosphate carboxylase large chain
G7: Ribulose bisphosphate carboxylase large chain
G8: Ribulose bisphosphate carboxylase large chain
H1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水1448
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I1: Ribulose bisphosphate carboxylase large chain
I2: Ribulose bisphosphate carboxylase large chain
I3: Ribulose bisphosphate carboxylase large chain
I4: Ribulose bisphosphate carboxylase large chain
I5: Ribulose bisphosphate carboxylase large chain
I6: Ribulose bisphosphate carboxylase large chain
I7: Ribulose bisphosphate carboxylase large chain
I8: Ribulose bisphosphate carboxylase large chain
J1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水18010
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K1: Ribulose bisphosphate carboxylase large chain
K2: Ribulose bisphosphate carboxylase large chain
K3: Ribulose bisphosphate carboxylase large chain
K4: Ribulose bisphosphate carboxylase large chain
K5: Ribulose bisphosphate carboxylase large chain
K6: Ribulose bisphosphate carboxylase large chain
K7: Ribulose bisphosphate carboxylase large chain
K8: Ribulose bisphosphate carboxylase large chain
L1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水18010
タイプ名称対称操作数
identity operation1_555x,y,z1
7
M1: Ribulose bisphosphate carboxylase large chain
M2: Ribulose bisphosphate carboxylase large chain
M3: Ribulose bisphosphate carboxylase large chain
M4: Ribulose bisphosphate carboxylase large chain
M5: Ribulose bisphosphate carboxylase large chain
M6: Ribulose bisphosphate carboxylase large chain
M7: Ribulose bisphosphate carboxylase large chain
M8: Ribulose bisphosphate carboxylase large chain
N1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水19811
タイプ名称対称操作数
identity operation1_555x,y,z1
8
O1: Ribulose bisphosphate carboxylase large chain
O2: Ribulose bisphosphate carboxylase large chain
O3: Ribulose bisphosphate carboxylase large chain
O4: Ribulose bisphosphate carboxylase large chain
O5: Ribulose bisphosphate carboxylase large chain
O6: Ribulose bisphosphate carboxylase large chain
O7: Ribulose bisphosphate carboxylase large chain
O8: Ribulose bisphosphate carboxylase large chain
P1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水18010
タイプ名称対称操作数
identity operation1_555x,y,z1
9
Q1: Ribulose bisphosphate carboxylase large chain
Q2: Ribulose bisphosphate carboxylase large chain
Q3: Ribulose bisphosphate carboxylase large chain
Q4: Ribulose bisphosphate carboxylase large chain
Q5: Ribulose bisphosphate carboxylase large chain
Q6: Ribulose bisphosphate carboxylase large chain
Q7: Ribulose bisphosphate carboxylase large chain
Q8: Ribulose bisphosphate carboxylase large chain
R1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
10
S1: Ribulose bisphosphate carboxylase large chain
S2: Ribulose bisphosphate carboxylase large chain
S3: Ribulose bisphosphate carboxylase large chain
S4: Ribulose bisphosphate carboxylase large chain
S5: Ribulose bisphosphate carboxylase large chain
S6: Ribulose bisphosphate carboxylase large chain
S7: Ribulose bisphosphate carboxylase large chain
S8: Ribulose bisphosphate carboxylase large chain
T1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,14032
ポリマ－491,09416
非ポリマー1,04716
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)217.918, 218.592, 310.273
Angle α, β, γ (deg.)69.400, 81.510, 65.500
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質 ...
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


分子量: 53031.273 Da / 分子数: 80 / 断片: RbcL / 変異: F345I / P415A / 由来タイプ: 組換発現
由来: (組換発現) Thermosynechococcus elongatus (strain BP-1) (バクテリア)
株: BP-1 / 遺伝子: cbbL, rbcL, tll1506 / プラスミド: pCDF-Duet / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q8DIS5, ribulose-bisphosphate carboxylase
#2: タンパク質 ...
DnaJ/Hsp40 cysteine-rich domain superfamily protein / Uncharacterized protein At3g47650 / Uncharacterized protein F1P2.200


分子量: 8355.468 Da / 分子数: 80 / 断片: mature protein, residues 53-136 / 変異: K56M / 由来タイプ: 組換発現
由来: (組換発現) Arabidopsis thaliana (シロイヌナズナ)
遺伝子: F1P2.200, At3g47650 / プラスミド: pCDF-Duet / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q9SN73
#3: 化合物...
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 160 / 由来タイプ: 合成 / 式: Zn
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 613 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.56 Å3/Da / 溶媒含有率: 52.02 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: 21 % PEG 3350 and 0.12M DL-malic acid pH 7.0

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID29 / 波長: 0.97 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2017年9月14日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97 Å / 相対比: 1
反射解像度: 2.63→198.29 Å / Num. obs: 1427774 / % possible obs: 98.5 % / 冗長度: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.09 / Rrim(I) all: 0.171 / Net I/σ(I): 6.2
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.63-2.673.71.215703980.4310.7371.42498.2
14.41-198.293.60.0486760.9990.0240.04798.3

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位相決定

位相決定手法: 分子置換
Phasing MRR rigid body: 0.614
最高解像度最低解像度
Rotation188.71 Å3 Å

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解析

ソフトウェア
名称バージョン分類
Aimless0.5.28データスケーリング
MOLREP11.4.06位相決定
REFMAC5.8.0155精密化
PDB_EXTRACT3.22データ抽出
XDSJun 1, 2017データ削減
精密化構造決定の手法: 分子置換
開始モデル: 3ZXW

3zxw


解像度: 2.63→50.01 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 18.454 / SU ML: 0.357 / SU R Cruickshank DPI: 1.3685 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 1.369 / ESU R Free: 0.359
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor反射数%反射Selection details
Rfree0.2742 71428 5 %RANDOM
Rwork0.2355 ---
obs0.2375 1356119 98.5 %-
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
原子変位パラメータBiso max: 197.43 Å2 / Biso mean: 57.241 Å2 / Biso min: 7.91 Å2
精密化ステップサイクル: final / 解像度: 2.63→50.01 Å
タンパク質核酸リガンド溶媒全体
原子数321026 0 160 613 321799
Biso mean--70.45 27.63 -
残基数----41600
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019328426
X-RAY DIFFRACTIONr_bond_other_d0.0020.02308412
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.948444862
X-RAY DIFFRACTIONr_angle_other_deg0.8893708344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.936541440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22523.66915036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2361553354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.87152240
X-RAY DIFFRACTIONr_chiral_restr0.0630.248000
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021377424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0277760
LS精密化 シェル解像度: 2.63→2.698 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.372 5239 -
Rwork0.362 99801 -
all-105040 -
obs--98.18 %

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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関連情報:EMDBヘッダ

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
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万見 (Yorodumi)

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