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- PDB-5d8b: Crystal structure of T. thermophilus ribosome containing a P-site... -

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基本情報

登録情報
データベース: PDB / ID: 5d8b
タイトルCrystal structure of T. thermophilus ribosome containing a P-site wobble mismatch
要素
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA16SリボソームRNA
  • 23S ribosomal RNA23SリボソームRNA
  • 5S ribosomal RNA5SリボソームRNA
  • mRNA伝令RNA
  • tRNA転移RNA
キーワードTRANSLATION (翻訳 (生物学)) / non-AUG initiation / wobble mismatch / cytosine-cytosine mismatch / ribosome (リボソーム)
機能・相同性
機能・相同性情報


ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / リボソーム / structural constituent of ribosome ...ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / 細胞質
類似検索 - 分子機能
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein
類似検索 - ドメイン・相同性
: / : / リボ核酸 / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 ...: / : / リボ核酸 / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19
類似検索 - 構成要素
生物種Thermus thermophilus (サーマス・サーモフィルス)
Thermus thermophilus HB27 (サーマス・サーモフィルス)
Escherichia coli (大腸菌)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.63 Å
データ登録者Svidritskiy, E. / Korostelev, A.A.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106105 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107465 米国
引用ジャーナル: Structure / 年: 2015
タイトル: Ribosome Structure Reveals Preservation of Active Sites in the Presence of a P-Site Wobble Mismatch.
著者: Svidritskiy, E. / Korostelev, A.A.
履歴
登録2015年8月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年10月14日Provider: repository / タイプ: Initial release
改定 1.12015年11月18日Group: Database references
改定 1.22017年9月13日Group: Author supporting evidence / Database references / Derived calculations
カテゴリ: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.32019年12月25日Group: Advisory / Author supporting evidence
カテゴリ: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization
改定 1.42023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
A: 50S ribosomal protein L2
B: 50S ribosomal protein L3
C: 50S ribosomal protein L4
D: 50S ribosomal protein L5
E: 50S ribosomal protein L6
F: 50S ribosomal protein L9
G: 50S ribosomal protein L11
H: 50S ribosomal protein L13
I: 50S ribosomal protein L14
J: 50S ribosomal protein L15
K: 50S ribosomal protein L16
L: 50S ribosomal protein L17
M: 50S ribosomal protein L18
N: 50S ribosomal protein L19
O: 50S ribosomal protein L20
P: 50S ribosomal protein L21
Q: 50S ribosomal protein L22
R: 50S ribosomal protein L23
S: 50S ribosomal protein L24
T: 50S ribosomal protein L25
U: 50S ribosomal protein L27
V: 50S ribosomal protein L28
W: 50S ribosomal protein L29
X: 50S ribosomal protein L30
Y: 50S ribosomal protein L32
Z: 50S ribosomal protein L33
AA: 50S ribosomal protein L34
BA: 50S ribosomal protein L35
CA: 30S ribosomal protein S2
DA: 30S ribosomal protein S3
EA: 30S ribosomal protein S4
FA: 30S ribosomal protein S5
GA: 30S ribosomal protein S6
HA: 30S ribosomal protein S7
IA: 30S ribosomal protein S8
JA: 30S ribosomal protein S9
KA: 30S ribosomal protein S10
LA: 30S ribosomal protein S11
MA: 30S ribosomal protein S12
NA: 30S ribosomal protein S13
OA: 30S ribosomal protein S14
PA: 30S ribosomal protein S15
QA: 30S ribosomal protein S16
RA: 30S ribosomal protein S17
SA: 30S ribosomal protein S18
TA: 30S ribosomal protein S19
UA: 30S ribosomal protein S20
VA: 30S ribosomal protein Thx
WA: 50S ribosomal protein L2
XA: 50S ribosomal protein L3
YA: 50S ribosomal protein L4
ZA: 50S ribosomal protein L5
AB: 50S ribosomal protein L6
BB: 50S ribosomal protein L9
CB: 50S ribosomal protein L11
DB: 50S ribosomal protein L13
EB: 50S ribosomal protein L14
FB: 50S ribosomal protein L15
GB: 50S ribosomal protein L16
HB: 50S ribosomal protein L17
IB: 50S ribosomal protein L18
JB: 50S ribosomal protein L19
KB: 50S ribosomal protein L20
LB: 50S ribosomal protein L21
MB: 50S ribosomal protein L22
NB: 50S ribosomal protein L23
OB: 50S ribosomal protein L24
PB: 50S ribosomal protein L25
QB: 50S ribosomal protein L27
RB: 50S ribosomal protein L28
SB: 50S ribosomal protein L29
TB: 50S ribosomal protein L30
UB: 50S ribosomal protein L32
VB: 50S ribosomal protein L33
WB: 50S ribosomal protein L34
XB: 50S ribosomal protein L35
YB: 30S ribosomal protein S2
ZB: 30S ribosomal protein S3
AC: 30S ribosomal protein S4
BC: 30S ribosomal protein S5
CC: 30S ribosomal protein S6
DC: 30S ribosomal protein S7
EC: 30S ribosomal protein S8
FC: 30S ribosomal protein S9
GC: 30S ribosomal protein S10
HC: 30S ribosomal protein S11
IC: 30S ribosomal protein S12
JC: 30S ribosomal protein S13
KC: 30S ribosomal protein S14
LC: 30S ribosomal protein S15
MC: 30S ribosomal protein S16
NC: 30S ribosomal protein S17
OC: 30S ribosomal protein S18
PC: 30S ribosomal protein S19
QC: 30S ribosomal protein S20
RC: 30S ribosomal protein Thx
SC: 50S ribosomal protein L31
TC: 50S ribosomal protein L31
UC: 16S ribosomal RNA
VC: 23S ribosomal RNA
WC: 5S ribosomal RNA
XC: tRNA
YC: 16S ribosomal RNA
ZC: 23S ribosomal RNA
AD: 5S ribosomal RNA
BD: tRNA
ED: tRNA
FD: tRNA
GD: mRNA
HD: mRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)4,505,4632332
ポリマ－4,451,293110
非ポリマー54,1702222
水0
1
A: 50S ribosomal protein L2
B: 50S ribosomal protein L3
C: 50S ribosomal protein L4
D: 50S ribosomal protein L5
E: 50S ribosomal protein L6
F: 50S ribosomal protein L9
G: 50S ribosomal protein L11
H: 50S ribosomal protein L13
I: 50S ribosomal protein L14
J: 50S ribosomal protein L15
K: 50S ribosomal protein L16
L: 50S ribosomal protein L17
M: 50S ribosomal protein L18
N: 50S ribosomal protein L19
O: 50S ribosomal protein L20
P: 50S ribosomal protein L21
Q: 50S ribosomal protein L22
R: 50S ribosomal protein L23
S: 50S ribosomal protein L24
T: 50S ribosomal protein L25
U: 50S ribosomal protein L27
V: 50S ribosomal protein L28
W: 50S ribosomal protein L29
X: 50S ribosomal protein L30
Y: 50S ribosomal protein L32
Z: 50S ribosomal protein L33
AA: 50S ribosomal protein L34
BA: 50S ribosomal protein L35
CA: 30S ribosomal protein S2
DA: 30S ribosomal protein S3
EA: 30S ribosomal protein S4
FA: 30S ribosomal protein S5
GA: 30S ribosomal protein S6
HA: 30S ribosomal protein S7
IA: 30S ribosomal protein S8
JA: 30S ribosomal protein S9
KA: 30S ribosomal protein S10
LA: 30S ribosomal protein S11
MA: 30S ribosomal protein S12
NA: 30S ribosomal protein S13
OA: 30S ribosomal protein S14
PA: 30S ribosomal protein S15
QA: 30S ribosomal protein S16
RA: 30S ribosomal protein S17
SA: 30S ribosomal protein S18
TA: 30S ribosomal protein S19
UA: 30S ribosomal protein S20
VA: 30S ribosomal protein Thx
SC: 50S ribosomal protein L31
UC: 16S ribosomal RNA
VC: 23S ribosomal RNA
WC: 5S ribosomal RNA
XC: tRNA
ED: tRNA
GD: mRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,251,7591126
ポリマ－2,225,64655
非ポリマー26,1131071
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
WA: 50S ribosomal protein L2
XA: 50S ribosomal protein L3
YA: 50S ribosomal protein L4
ZA: 50S ribosomal protein L5
AB: 50S ribosomal protein L6
BB: 50S ribosomal protein L9
CB: 50S ribosomal protein L11
DB: 50S ribosomal protein L13
EB: 50S ribosomal protein L14
FB: 50S ribosomal protein L15
GB: 50S ribosomal protein L16
HB: 50S ribosomal protein L17
IB: 50S ribosomal protein L18
JB: 50S ribosomal protein L19
KB: 50S ribosomal protein L20
LB: 50S ribosomal protein L21
MB: 50S ribosomal protein L22
NB: 50S ribosomal protein L23
OB: 50S ribosomal protein L24
PB: 50S ribosomal protein L25
QB: 50S ribosomal protein L27
RB: 50S ribosomal protein L28
SB: 50S ribosomal protein L29
TB: 50S ribosomal protein L30
UB: 50S ribosomal protein L32
VB: 50S ribosomal protein L33
WB: 50S ribosomal protein L34
XB: 50S ribosomal protein L35
YB: 30S ribosomal protein S2
ZB: 30S ribosomal protein S3
AC: 30S ribosomal protein S4
BC: 30S ribosomal protein S5
CC: 30S ribosomal protein S6
DC: 30S ribosomal protein S7
EC: 30S ribosomal protein S8
FC: 30S ribosomal protein S9
GC: 30S ribosomal protein S10
HC: 30S ribosomal protein S11
IC: 30S ribosomal protein S12
JC: 30S ribosomal protein S13
KC: 30S ribosomal protein S14
LC: 30S ribosomal protein S15
MC: 30S ribosomal protein S16
NC: 30S ribosomal protein S17
OC: 30S ribosomal protein S18
PC: 30S ribosomal protein S19
QC: 30S ribosomal protein S20
RC: 30S ribosomal protein Thx
TC: 50S ribosomal protein L31
YC: 16S ribosomal RNA
ZC: 23S ribosomal RNA
AD: 5S ribosomal RNA
BD: tRNA
FD: tRNA
HD: mRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,253,7041206
ポリマ－2,225,64655
非ポリマー28,0571151
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)211.980, 453.750, 620.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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要素

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50S ribosomal protein ... , 29種, 58分子 AWABXACYADZAEABFBBGCBHDBIEBJFBKGBLHBMIBNJBOKB...

#1: タンパク質 50S ribosomal protein L2 /


分子量: 29828.604 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I07, UniProt: P60405*PLUS
#2: タンパク質 50S ribosomal protein L3 /


分子量: 22450.213 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I04, UniProt: Q5SHN8*PLUS
#3: タンパク質 50S ribosomal protein L4 /


分子量: 22744.279 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I05, UniProt: Q5SHN9*PLUS
#4: タンパク質 50S ribosomal protein L5 /


分子量: 21075.623 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I16, UniProt: Q5SHQ0*PLUS
#5: タンパク質 50S ribosomal protein L6 /


分子量: 19568.926 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I19, UniProt: P0DOY8*PLUS
#6: タンパク質 50S ribosomal protein L9 /


分子量: 16436.205 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72GV5, UniProt: Q5SLQ1*PLUS
#7: タンパク質 50S ribosomal protein L11 /


分子量: 15526.111 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62442, UniProt: Q5SLP6*PLUS
#8: タンパク質 50S ribosomal protein L13 /


分子量: 15927.903 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72IN1, UniProt: P60488*PLUS
#9: タンパク質 50S ribosomal protein L14 /


分子量: 13309.586 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I14, UniProt: Q5SHP8*PLUS
#10: タンパク質 50S ribosomal protein L15 /


分子量: 16319.142 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I23, UniProt: Q5SHQ7*PLUS
#11: タンパク質 50S ribosomal protein L16 /


分子量: 15977.909 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I11, UniProt: P60489*PLUS
#12: タンパク質 50S ribosomal protein L17 /


分子量: 13750.148 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I33, UniProt: Q9Z9H5*PLUS
#13: タンパク質 50S ribosomal protein L18 /


分子量: 12639.845 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I20, UniProt: Q5SHQ4*PLUS
#14: タンパク質 50S ribosomal protein L19 /


分子量: 17217.867 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72JU9, UniProt: P60490*PLUS
#15: タンパク質 50S ribosomal protein L20 /


分子量: 13779.275 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72L76, UniProt: P60491*PLUS
#16: タンパク質 50S ribosomal protein L21 /


分子量: 11069.153 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72HR2, UniProt: P60492*PLUS
#17: タンパク質 50S ribosomal protein L22 /


分子量: 12808.055 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I09, UniProt: Q5SHP3*PLUS
#18: タンパク質 50S ribosomal protein L23 /


分子量: 10759.808 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I06, UniProt: Q5SHP0*PLUS
#19: タンパク質 50S ribosomal protein L24 /


分子量: 12085.611 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I15, UniProt: Q5SHP9*PLUS
#20: タンパク質 50S ribosomal protein L25 /


分子量: 23238.572 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72IA7, UniProt: Q5SHZ1*PLUS
#21: タンパク質 50S ribosomal protein L27 /


分子量: 9501.061 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72HR3, UniProt: P60493*PLUS
#22: タンパク質 50S ribosomal protein L28 /


分子量: 11032.174 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72G84, UniProt: P60494*PLUS
#23: タンパク質 50S ribosomal protein L29 /


分子量: 8670.258 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I12, UniProt: Q5SHP6*PLUS
#24: タンパク質 50S ribosomal protein L30 /


分子量: 6799.126 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72I22, UniProt: Q5SHQ6*PLUS
#25: タンパク質 50S ribosomal protein L32 /


分子量: 6734.104 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62652, UniProt: P80339*PLUS
#26: タンパク質 50S ribosomal protein L33 /


分子量: 6632.896 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72GW3, UniProt: P35871*PLUS
#27: タンパク質・ペプチド 50S ribosomal protein L34 /


分子量: 6132.449 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80340
#28: タンパク質 50S ribosomal protein L35 /


分子量: 7506.178 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72L77, UniProt: Q5SKU1*PLUS
#49: タンパク質 50S ribosomal protein L31 /


分子量: 8300.543 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: Q72JR0, UniProt: Q5SJE1*PLUS

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30S ribosomal protein ... , 20種, 40分子 CAYBDAZBEAACFABCGACCHADCIAECJAFCKAGCLAHCMAICNAJCOAKCPALCQAMC...

#29: タンパク質 30S ribosomal protein S2 /


分子量: 29317.703 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62662, UniProt: P80371*PLUS
#30: タンパク質 30S ribosomal protein S3 /


分子量: 26751.076 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62663, UniProt: P80372*PLUS
#31: タンパク質 30S ribosomal protein S4 /


分子量: 24373.447 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62664, UniProt: P80373*PLUS
#32: タンパク質 30S ribosomal protein S5 /


分子量: 17583.416 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62665, UniProt: Q5SHQ5*PLUS
#33: タンパク質 30S ribosomal protein S6 /


分子量: 11988.753 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62666, UniProt: Q5SLP8*PLUS
#34: タンパク質 30S ribosomal protein S7 /


分子量: 18050.973 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62667, UniProt: P17291*PLUS
#35: タンパク質 30S ribosomal protein S8 /


分子量: 15868.570 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62668, UniProt: P0DOY9*PLUS
#36: タンパク質 30S ribosomal protein S9 /


分子量: 14429.661 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62669, UniProt: P80374*PLUS
#37: タンパク質 30S ribosomal protein S10 /


分子量: 11954.968 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62653, UniProt: Q5SHN7*PLUS
#38: タンパク質 30S ribosomal protein S11 /


分子量: 13737.868 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62654, UniProt: P80376*PLUS
#39: タンパク質 30S ribosomal protein S12 /


分子量: 14637.384 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P61941, UniProt: Q5SHN3*PLUS
#40: タンパク質 30S ribosomal protein S13 /


分子量: 14338.861 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62655, UniProt: P80377*PLUS
#41: タンパク質 30S ribosomal protein S14 /


分子量: 7158.725 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62656, UniProt: P0DOY6*PLUS
#42: タンパク質 30S ribosomal protein S15 /


分子量: 10578.407 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62657, UniProt: Q5SJ76*PLUS
#43: タンパク質 30S ribosomal protein S16 /


分子量: 10409.983 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62238, UniProt: Q5SJH3*PLUS
#44: タンパク質 30S ribosomal protein S17 /


分子量: 12324.670 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62658, UniProt: P0DOY7*PLUS
#45: タンパク質 30S ribosomal protein S18 /


分子量: 10258.299 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62659, UniProt: Q5SLQ0*PLUS
#46: タンパク質 30S ribosomal protein S19 /


分子量: 10605.464 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62660, UniProt: Q5SHP2*PLUS
#47: タンパク質 30S ribosomal protein S20 /


分子量: 11722.116 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62661, UniProt: P80380*PLUS
#48: タンパク質・ペプチド 30S ribosomal protein Thx / リボソーム


分子量: 3350.030 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (サーマス・サーモフィルス)
株: HB27 / ATCC BAA-163 / DSM 7039 / 参照: UniProt: P62613, UniProt: Q5SIH3*PLUS

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RNA鎖 , 5種, 12分子 UCYCVCZCWCADXCBDEDFDGDHD

#50: RNA鎖 16S ribosomal RNA / 16SリボソームRNA


分子量: 490001.062 Da / 分子数: 2 / Fragment: GB residues 1311714-1310206 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus HB27 (サーマス・サーモフィルス)
参照: GenBank: 46197919
#51: RNA鎖 23S ribosomal RNA / 23SリボソームRNA


分子量: 940743.812 Da / 分子数: 2 / Fragment: GB residues 1534490-1537382 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus HB27 (サーマス・サーモフィルス)
参照: GenBank: 46197919
#52: RNA鎖 5S ribosomal RNA / 5SリボソームRNA


分子量: 39211.414 Da / 分子数: 2 / Fragment: GB residues 1537461-1537581 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus HB27 (サーマス・サーモフィルス)
参照: GenBank: 46197919
#53: RNA鎖
tRNA / 転移RNA


分子量: 24802.785 Da / 分子数: 4 / Fragment: GB residues 3822935-3823011 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 参照: GenBank: 899721066
#54: RNA鎖 mRNA / 伝令RNA


分子量: 8822.432 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 2種, 2222分子

#55: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2218 / 由来タイプ: 合成 / 式: Mg
#56: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn

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実験情報

-
実験

実験手法: X線回折

-
試料調製

結晶マシュー密度: 3.35 Å3/Da / 溶媒含有率: 63.32 %
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 3.1 uL 70S*mRNA*tRNAfMet complex + 3.1 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate), reservoir: 300 uL 0.5-0.7 M sodium ...詳細: 3.1 uL 70S*mRNA*tRNAfMet complex + 3.1 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate), reservoir: 300 uL 0.5-0.7 M sodium chloride, 3-fold molar excess of E. coli release factor 1 and 650 uM blasticidin S added during complex formation to stabilize the complex

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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: APS / ビームライン: 23-ID-B / 波長: 1.033 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2013年11月30日
放射モノクロメーター: double crystal Si(111) / 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: 1.033 Å / 相対比: 1
反射解像度: 3.63→60 Å / Num. obs: 661200 / % possible obs: 99.3 % / 冗長度: 10.5 % / Net I/σ(I): 5.7

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
XSCALEデータスケーリング
XDSデータ削減
Blu-Iceデータ収集
PHENIX1.9-1692位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 4V9Q

4v9q


解像度: 3.63→60 Å / 交差検証法: FREE R-VALUE
Rfactor反射数%反射
Rfree0.287 6612 -
Rwork0.268 --
obs-661197 99.3 %
原子変位パラメータBiso max: 138.73 Å2 / Biso mean: 102.7818 Å2 / Biso min: 76.15 Å2
精密化ステップサイクル: final / 解像度: 3.63→60 Å
タンパク質核酸リガンド溶媒全体
原子数92746 200666 0 0 293412
残基数----271
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1563-0.06490.03970.46780.14880.4810.0016-0.0426-0.0330.04240.0985-0.06130.0481-0.1737-0.1110.7099-0.0754-0.06941.12380.00690.7759-17.082135.1152167.9003
20.3180.02560.15160.3325-0.00180.4694-0.0422-0.05170.073-0.03970.00480.07810.008-0.11260.04710.56010.0217-0.05580.67780.04710.7461-74.6277-57.176921.4443
30.9391-0.219-0.26931.3824-0.25411.3414-0.07170.82030.1635-0.87210.48091.8287-0.3523-0.9727-0.42852.59780.2634-0.49092.60180.48742.6742-53.5244194.214988.4102
40.05580.08050.06940.17330.09350.10761.32410.45150.2183-0.5807-0.07740.88540.1347-0.0649-0.69473.54-0.71370.37217.73650.5195.0183-93.523264.7297166.6141
50.27070.1302-0.16730.95620.44510.99220.1744-0.42480.53151.2526-0.62991.2183-0.7378-1.42170.51943.0540.43220.4942.1015-0.50942.8839-105.033821.892583.8642
60.0099-0.0016-0.00950.38030.18190.0740.2654-0.56552.0188-0.3762-0.65450.5214-1.5455-0.4160.41023.1294-0.36580.24443.6148-0.23645.1556-152.4415-48.0091-47.9791
71.12880.02240.01310.31420.11710.00870.1389-0.2653-0.2126-0.3628-0.17280.62220.0228-0.36370.01041.5948-0.0305-0.63352.1689-0.24041.9437-97.2843101.739571.1468
80.72440.1230.16240.0501-0.05620.1163-0.1135-0.0660.0989-0.09110.04460.2742-0.4218-0.50180.08561.76940.7024-0.5671.89980.09332.3609-149.002245.4611-6.6632
90.1821-0.06870.01530.41690.08470.31490.09290.1591-0.1318-0.2215-0.03870.0050.1087-0.0375-0.06921.243-0.1603-0.12951.2912-0.16251.0082-14.013168.136695.6005
100.4478-0.1369-0.01530.72860.0310.51-0.09220.2950.3808-0.6553-0.0201-0.0087-0.40880.02230.1191.7531-0.1975-0.43051.01190.42671.4164-68.486316.7693-43.236
110.4516-0.076-0.11270.712-0.05230.73710.00480.35310.1712-0.14680.2833-0.1140.02470.031-0.2150.9608-0.06330.11871.1504-0.03320.67141.2784144.2793113.9668
120.7642-0.0633-0.51450.8408-0.05470.2521-0.1645-0.2691-0.19310.3621-0.1591-0.12130.2628-0.14110.19831.4728-0.0654-0.31471.330.08980.8073-10.767472.3839194.4882
130.69010.2756-0.17341.12530.81290.67820.06110.15520.33050.1542-0.0631-0.1055-0.1516-0.3714-0.09451.02430.2501-0.17910.9487-0.11110.8896-19.6625184.7764207.0179
140.39240.19120.03651.40350.17830.98430.1416-0.59450.1649-0.40610.16920.64970.3345-0.2011-0.30561.1064-0.0542-0.1732.69950.00271.7232-121.3115144.3463130.2249
150.7207-0.12020.41051.1355-0.20440.2445-0.2332-0.4869-0.11450.27070.55531.11980.5245-0.4189-0.13332.3752-0.54360.51831.82080.31991.9926-65.935856.1444197.6628
16-0.0149-0.0113-0.02550.26470.0599-0.0039-0.10260.22630.2449-0.4056-0.37220.07570.3589-0.1870.53582.2526-0.05950.27260.89710.16221.80492.0027220.765399.8798
170.139-0.2608-0.31140.61650.3550.6232-0.16230.1995-0.19090.26320.1570.09340.38530.0079-0.10661.4094-0.26470.0831.40780.12710.7989-42.399592.9227218.5677
181.0286-0.34010.2621.54070.26550.99220.3690.1397-0.130.3054-0.1091-0.05740.3049-0.2042-0.20311.382-0.0712-0.34751.1906-0.24850.8534-16.86766.0837151.098
190.12760.28180.27240.59490.47710.34110.1574-0.44160.3021-0.1309-0.32460.1559-0.3194-0.30320.29311.35290.2528-0.10421.5583-0.12861.1718-48.0276187.0602182.6981
200.4996-0.05920.21551.21680.02170.69680.0501-0.1196-0.39830.27190.0198-0.41920.1737-0.4240.06061.1582-0.4064-0.07752.46970.01951.7921-82.5778107.0207168.6192
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1060.65790.43171.09720.30780.74811.9067-0.0497-0.1990.2963-0.4002-0.31560.958-0.3125-0.64320.36942.9114-0.2196-0.78293.4401-0.06034.0508-185.55762.212241.3861
1070.56920.35980.34040.713-0.14740.5671-0.1527-0.1703-0.23580.08360.31960.7922-0.0904-1.238-0.29041.10950.00660.17573.0009-0.10371.7593-113.7075143.3553171.2385
1080.0092-0.0138-0.0247-0.00610.00970.00040.23350.23570.66280.0958-0.14390.3567-0.2944-0.6918-0.02592.7148-0.2755-0.08683.5628-0.09184.3992-103.996358.0783153.0121
109-0.0092-0.03080.00170.00750.02040.00890.01970.27820.02970.4124-0.1540.47890.307-0.59640.14573.72340.20040.25342.4885-0.37394.11-161.787-33.2771-53.2789
1100.237-0.2613-0.3980.43470.56430.7481-0.3802-0.19690.30610.09230.03260.7972-0.3798-0.29270.42722.4620.3886-0.24593.48830.1752.7453-66.1196162.8894108.3535
1114.27850.78333.68193.2612-1.05764.13920.2209-0.0542-0.987-0.1315-0.07550.2141.0664-0.1449-0.15733.7875-0.2682-0.07143.1428-0.35153.6494-65.8752130.453687.7179
1120.00130.0057-0.00240.05070.00790.0251-0.0191-0.0650.1728-0.1475-0.04670.3241-0.2916-0.12540.08382.8104-0.1055-0.12863.1563-0.49753.6062-56.2337121.138686.3967
1133.88860.0034-0.64443.337-2.18173.1511-0.05330.0418-0.2149-0.2715-0.0810.18470.143-0.19150.09421.20360.3022-0.2461.86290.13321.9443-58.4954107.050591.5178
1141.62.73982.49285.98945.15874.4942-0.20111.6559-2.618-2.58260.2791-5.01831.13372.5428-0.07132.04030.06540.14692.00820.05032.9717-61.008392.444193.9905
1150.5343-0.2689-0.69641.38870.33191.64230.0953-0.5140.2490.61550.32870.4871-0.098-0.2212-0.52391.38240.0403-0.09142.8032-0.26062.1409-71.5633125.8766126.9335
1160.05150.04040.18020.03980.15990.6265-0.1074-0.087-0.039-0.0247-0.09430.15760.0397-0.10660.11551.3338-0.4435-0.3252.14630.09161.8234-68.823110.545691.6842
1170.8014-0.3361-0.71452.152-0.34160.8599-0.1369-0.08190.04250.0051-0.00560.1277-0.00390.09220.14383.40780.4019-0.20773.7111-0.1942.5557-40.6923122.3898154.7717
1180.4558-0.6715-0.36280.59380.31580.47080.07280.0460.11-0.06940.09050.23520.1236-0.3706-0.14910.8804-0.0209-0.17122.0429-0.00051.7886-171.1013-54.269231.4201
1190.20930.2538-0.02850.2692-0.12360.2422-0.2983-0.4250.1346-0.0551-0.38240.48490.1272-0.48930.42712.80330.2956-0.22542.8-0.27123.633-119.25383.449252.7007
1202.2982-1.89711.74862.8249-2.41263.4630.0620.0549-0.3402-0.6996-0.11670.35720.22330.04210.07693.96090.074-0.48264.25970.17574.0287-118.477625.59621.2688
1210.0045-0.00230.03670.02490.04390.5639-0.1467-0.39380.03830.0755-0.08390.2156-0.2069-0.10560.22462.80980.0036-0.45373.335-0.19523.068-108.572326.769511.2198
1220.1136-0.0587-0.33550.04160.19871.2998-0.15380.43060.3203-0.8065-0.13850.4449-0.5313-0.15240.26931.3931-0.0206-0.64131.7749-0.20231.632-111.410522.3835-3.0038
1231.86590.11571.83381.8078-0.92722.8359-0.4232.05771.5108-1.00440.1-2.5248-3.10214.65960.3132.4509-0.1247-0.58862.6828-0.3341.8889-114.35720.6631-17.6421
1240.74940.8426-0.22220.9216-0.3480.586-0.4042-0.2725-0.06810.07360.24260.07730.1115-0.47110.30411.24960.1266-0.20691.90260.39432.4633-126.442-12.503214.9813
1252.48560.9369-1.41832.61081.84633.3304-0.1064-0.0873-0.4693-0.1017-0.1369-0.32370.44190.4650.20042.9522-0.00120.56542.77020.18473.048-97.6419-42.09229.7514
1260.3628-0.0836-0.07960.1195-0.20041.98890.13040.14730.1617-0.4423-0.23060.1808-0.0325-0.02080.13851.40880.4469-0.92471.77190.11122.6239-121.66622.83390.6808
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain VC and not (resid 2094:2190 or resid 1050:1104))V0
2X-RAY DIFFRACTION2(chain ZC and not (resid 2094:2190 or resid 1050:1104))Z0
3X-RAY DIFFRACTION3(chain VC and resi 2094:2190)V0
4X-RAY DIFFRACTION4(chain VC and resi 1050:1104)V0
5X-RAY DIFFRACTION5(chain ZC and resi 2094:2190)Z0
6X-RAY DIFFRACTION6(chain ZC and resi 1050:1104)Z0
7X-RAY DIFFRACTION7(chain UC and resid 925:1391)U0
8X-RAY DIFFRACTION8(chain YC and resid 925:1391)Y0
9X-RAY DIFFRACTION9(chain UC and not resid 925:1391)U0
10X-RAY DIFFRACTION10(chain YC and not resid 925:1391)Y0
11X-RAY DIFFRACTION11(chain A)A0
12X-RAY DIFFRACTION12(chain B)B0
13X-RAY DIFFRACTION13(chain C)C0
14X-RAY DIFFRACTION14(chain D)D0
15X-RAY DIFFRACTION15(chain E)E0
16X-RAY DIFFRACTION16(chain F)F0
17X-RAY DIFFRACTION17(chain H)H0
18X-RAY DIFFRACTION18(chain I)I0
19X-RAY DIFFRACTION19(chain J)J0
20X-RAY DIFFRACTION20(chain K)K0
21X-RAY DIFFRACTION21(chain L)L0
22X-RAY DIFFRACTION22(chain M)M0
23X-RAY DIFFRACTION23(chain N)N0
24X-RAY DIFFRACTION24(chain O)O0
25X-RAY DIFFRACTION25(chain P)P0
26X-RAY DIFFRACTION26(chain Q)Q0
27X-RAY DIFFRACTION27(chain R)R0
28X-RAY DIFFRACTION28(chain S)S0
29X-RAY DIFFRACTION29(chain T)T0
30X-RAY DIFFRACTION30(chain U)U0
31X-RAY DIFFRACTION31(chain V)V0
32X-RAY DIFFRACTION32(chain W)W0
33X-RAY DIFFRACTION33(chain X)X0
34X-RAY DIFFRACTION34(chain Y)Y0
35X-RAY DIFFRACTION35(chain Z)Z0
36X-RAY DIFFRACTION36(chain AA)A0
37X-RAY DIFFRACTION37(chain BA)B0
38X-RAY DIFFRACTION38(chain CA)C0
39X-RAY DIFFRACTION39(chain DA)D0
40X-RAY DIFFRACTION40(chain EA)E0
41X-RAY DIFFRACTION41(chain FA)F0
42X-RAY DIFFRACTION42(chain GA)G0
43X-RAY DIFFRACTION43(chain HA)H0
44X-RAY DIFFRACTION44(chain IA)I0
45X-RAY DIFFRACTION45(chain JA)J0
46X-RAY DIFFRACTION46(chain KA)K0
47X-RAY DIFFRACTION47(chain LA)L0
48X-RAY DIFFRACTION48(chain MA)M0
49X-RAY DIFFRACTION49(chain NA)N0
50X-RAY DIFFRACTION50(chain OA)O0
51X-RAY DIFFRACTION51(chain PA)P0
52X-RAY DIFFRACTION52(chain QA)Q0
53X-RAY DIFFRACTION53(chain RA)R0
54X-RAY DIFFRACTION54(chain SA)S0
55X-RAY DIFFRACTION55(chain TA)T0
56X-RAY DIFFRACTION56(chain UA)U0
57X-RAY DIFFRACTION57(chain VA)V0
58X-RAY DIFFRACTION58(chain WA)W0
59X-RAY DIFFRACTION59(chain XA)X0
60X-RAY DIFFRACTION60(chain YA)Y0
61X-RAY DIFFRACTION61(chain ZA)Z0
62X-RAY DIFFRACTION62(chain AB)A0
63X-RAY DIFFRACTION63(chain BB)B0
64X-RAY DIFFRACTION64(chain DB)D0
65X-RAY DIFFRACTION65(chain EB)E0
66X-RAY DIFFRACTION66(chain FB)F0
67X-RAY DIFFRACTION67(chain GB)G0
68X-RAY DIFFRACTION68(chain HB)H0
69X-RAY DIFFRACTION69(chain IB)I0
70X-RAY DIFFRACTION70(chain JB)J0
71X-RAY DIFFRACTION71(chain KB)K0
72X-RAY DIFFRACTION72(chain LB)L0
73X-RAY DIFFRACTION73(chain MB)M0
74X-RAY DIFFRACTION74(chain NB)N0
75X-RAY DIFFRACTION75(chain OB)O0
76X-RAY DIFFRACTION76(chain PB)P0
77X-RAY DIFFRACTION77(chain QB)Q0
78X-RAY DIFFRACTION78(chain RB)R0
79X-RAY DIFFRACTION79(chain SB)S0
80X-RAY DIFFRACTION80(chain TB)T0
81X-RAY DIFFRACTION81(chain UB)U0
82X-RAY DIFFRACTION82(chain VB)V0
83X-RAY DIFFRACTION83(chain WB)W0
84X-RAY DIFFRACTION84(chain XB)X0
85X-RAY DIFFRACTION85(chain YB)Y0
86X-RAY DIFFRACTION86(chain ZB)Z0
87X-RAY DIFFRACTION87(chain AC)A0
88X-RAY DIFFRACTION88(chain BC)B0
89X-RAY DIFFRACTION89(chain CC)C0
90X-RAY DIFFRACTION90(chain DC)D0
91X-RAY DIFFRACTION91(chain EC)E0
92X-RAY DIFFRACTION92(chain FC)F0
93X-RAY DIFFRACTION93(chain GC)G0
94X-RAY DIFFRACTION94(chain HC)H0
95X-RAY DIFFRACTION95(chain IC)I0
96X-RAY DIFFRACTION96(chain JC)J0
97X-RAY DIFFRACTION97(chain KC)K0
98X-RAY DIFFRACTION98(chain LC)L0
99X-RAY DIFFRACTION99(chain MC)M0
100X-RAY DIFFRACTION100(chain NC)N0
101X-RAY DIFFRACTION101(chain OC)O0
102X-RAY DIFFRACTION102(chain PC)P0
103X-RAY DIFFRACTION103(chain QC)Q0
104X-RAY DIFFRACTION104(chain RC)R0
105X-RAY DIFFRACTION105(chain SC)S0
106X-RAY DIFFRACTION106(chain TC)T0
107X-RAY DIFFRACTION107(chain WC)W0
108X-RAY DIFFRACTION108(chain G)G0
109X-RAY DIFFRACTION109(chain CB)C0
110X-RAY DIFFRACTION110(chain XC and not resid 32:38)X0
111X-RAY DIFFRACTION111(chain XC and resi 32:38)X0
112X-RAY DIFFRACTION112(chain GD and not resid 16:25)G0
113X-RAY DIFFRACTION113(chain GD and resi 16:18)G0
114X-RAY DIFFRACTION114(chain GD and resi 19:20)G0
115X-RAY DIFFRACTION115(chain ED and (resid 1:31 or resid 39:72))E0
116X-RAY DIFFRACTION116(chain ED and resi 32:38)E0
117X-RAY DIFFRACTION117(chain ED and resi 73:76)E0
118X-RAY DIFFRACTION118(chain AD)A0
119X-RAY DIFFRACTION119(chain BD and not resid 32:38)B0
120X-RAY DIFFRACTION120(chain BD and resi 32:38)B0
121X-RAY DIFFRACTION121(chain HD and resid 13:15)H0
122X-RAY DIFFRACTION122(chain HD and resi 16:18)H0
123X-RAY DIFFRACTION123(chain HD and resi 19:20)H0
124X-RAY DIFFRACTION124(chain FD and (resid 1:31 or resid 39:72))F0
125X-RAY DIFFRACTION125(chain FD and resi 73:76)F0
126X-RAY DIFFRACTION126(chain FD and resi 32:38)F0

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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

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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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

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

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

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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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

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 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。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る