[English] 日本語
Yorodumi
- PDB-4v9f: The re-refined crystal structure of the Haloarcula marismortui la... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v9f
TitleThe re-refined crystal structure of the Haloarcula marismortui large ribosomal subunit at 2.4 Angstrom resolution: more complete structure of the L7/L12 and L1 stalk, L5 and LX proteins
Components
  • (50S ribosomal protein ...) x 31
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
KeywordsRIBOSOME / 50S ribosomal subunit / ribonucleoprotein / ribosomal protein / RNA binding / tRNA binding / metal binding
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding
Similarity search - Function
Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50S ribosomal protein L10, archaea / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea ...Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50S ribosomal protein L10, archaea / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein L24e / DNA repair Rad51/transcription factor NusA, alpha-helical / Ribosomal protein L2, archaeal-type / Helix-hairpin-helix domain / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e / Ribosomal protein L37ae / Ribosomal protein L31e, conserved site / Ribosomal L37ae protein family / Ribosomal protein L31e signature. / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L15e, conserved site / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal protein L15e signature. / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L37ae/L37e / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal protein L32 / Ribosomal_L32e
Similarity search - Domain/homology
ACETIC ACID / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 ...ACETIC ACID / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / 50S ribosomal protein L18Ae / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsGabdulkhakov, A.
CitationJournal: Science / Year: 2000
Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4HUB, 4I4M
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jun 28, 2017Group: Database references / Category: struct_ref_seq
Item: _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end ..._struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 1.3Jul 17, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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
Remark 0THIS ENTRY 4HUB REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1FFKSF) ...THIS ENTRY 4HUB REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1FFKSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1FFK: N.BAN, P.NISSEN, J.HANSEN, P.B.MOORE, T.A.STEITZ

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: 23S Ribosomal RNA
9: 5S Ribosomal RNA
A: 50S ribosomal protein L2P
B: 50S ribosomal protein L3P
C: 50S ribosomal protein L4P
D: 50S ribosomal protein L5P
E: 50S ribosomal protein L6P
F: 50S ribosomal protein L7Ae
G: 50S ribosomal protein L10E
H: 50S ribosomal protein L10e
I: 50S ribosomal protein L11P
J: 50S ribosomal protein L13P
K: 50S ribosomal protein L14P
L: 50S ribosomal protein L15P
M: 50S ribosomal protein L15e
N: 50S ribosomal protein L18P
O: 50S ribosomal protein L18e
P: 50S ribosomal protein L19e
Q: 50S ribosomal protein L21e
R: 50S ribosomal protein L22P
S: 50S ribosomal protein L23P
T: 50S ribosomal protein L24P
U: 50S ribosomal protein L24e
V: 50S ribosomal protein L29P
W: 50S ribosomal protein L30P
X: 50S ribosomal protein L31e
Y: 50S ribosomal protein L32e
Z: 50S ribosomal protein L37Ae
1: 50S ribosomal protein L37e
2: 50S ribosomal protein L39e
3: 50S ribosomal protein L44e
4: 50S ribosomal protein L12
5: 50S ribosomal protein L12
6: 50S ribosomal protein LX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,486,403299
Polymers1,479,11234
Non-polymers7,291265
Water139,5267745
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.660, 299.670, 573.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
RNA chain , 2 types, 2 molecules 09

#1: RNA chain 23S Ribosomal RNA


Mass: 942258.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809
#2: RNA chain 5S Ribosomal RNA


Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809

+
50S ribosomal protein ... , 31 types, 32 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ123456

#3: Protein 50S ribosomal protein L2P / Hl4 / Hmal2


Mass: 25354.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P20276
#4: Protein 50S ribosomal protein L3P / Hl1 / Hmal3


Mass: 37396.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P20279
#5: Protein 50S ribosomal protein L4P / Hl6 / Hmal4


Mass: 26457.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P12735
#6: Protein 50S ribosomal protein L5P / Hl13 / Hmal5


Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P14124
#7: Protein 50S ribosomal protein L6P / Hl10 / Hmal6


Mass: 19961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P14135
#8: Protein 50S ribosomal protein L7Ae / Hs6


Mass: 12791.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P12743
#9: Protein 50S ribosomal protein L10E / Ribosomal protein L10 / Acidic ribosomal protein P0 homolog / HMal10 / L10E


Mass: 26454.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P15825
#10: Protein 50S ribosomal protein L10e


Mass: 19942.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P60617
#11: Protein 50S ribosomal protein L11P / Hmal11


Mass: 17097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P14122
#12: Protein 50S ribosomal protein L13P / Hmal13


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P29198
#13: Protein 50S ribosomal protein L14P / Hl27 / Hmal14


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P22450
#14: Protein 50S ribosomal protein L15P / Hl9 / Hmal15


Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P12737
#15: Protein 50S ribosomal protein L15e / 50S ribosomal protein LC12


Mass: 22404.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P60618
#16: Protein 50S ribosomal protein L18P / Hl12 / Hmal18


Mass: 20640.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P14123
#17: Protein 50S ribosomal protein L18e / Hl29 / L19


Mass: 12438.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P12733
#18: Protein 50S ribosomal protein L19e / Hl24 / Hmal19


Mass: 16796.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P14119
#19: Protein 50S ribosomal protein L21e / Hl31


Mass: 10567.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P12734
#20: Protein 50S ribosomal protein L22P / Hl23 / Hmal22


Mass: 16966.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P10970
#21: Protein 50S ribosomal protein L23P / Hl25 / Hmal23 / L21


Mass: 9612.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P12732
#22: Protein 50S ribosomal protein L24P / Hl15 / Hl16 / Hmal24


Mass: 13670.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P10972
#23: Protein 50S ribosomal protein L24e / Hl21/Hl22


Mass: 7364.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P14116
#24: Protein 50S ribosomal protein L29P / Hl33 / Hmal29


Mass: 7889.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P10971
#25: Protein 50S ribosomal protein L30P / Hl16 / Hl20 / Hmal30


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P14121
#26: Protein 50S ribosomal protein L31e / Hl30 / L34


Mass: 10384.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P18138
#27: Protein 50S ribosomal protein L32e / Hl5


Mass: 26455.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P12736
#28: Protein 50S ribosomal protein L37Ae


Mass: 10189.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P60619
#29: Protein 50S ribosomal protein L37e / L35e


Mass: 6330.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P32410
#30: Protein/peptide 50S ribosomal protein L39e / Hl39e / Hl46e


Mass: 6133.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P22452
#31: Protein 50S ribosomal protein L44e / HLA / La


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P32411
#32: Protein 50S ribosomal protein L12 / Hmal12


Mass: 5975.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809
#33: Protein 50S ribosomal protein LX / HL32


Mass: 6394.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / References: UniProt: P14125

-
Non-polymers , 7 types, 8010 molecules

#34: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 138 / Source method: obtained synthetically / Formula: Mg
#35: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#36: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 85 / Source method: obtained synthetically / Formula: Na
#37: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Cl
#38: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#39: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#40: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7745 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE SEQUENCES OF CHAINS 4 AND 5 AND THE C-TERMINAL DOMAIN OF CHAIN G ARE UNKNOWN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.11 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1FFK.

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FFK

1ffk


Resolution: 2.404→85.478 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 6672 1 %RANDOM
Rwork0.1656 ---
all0.167 666777 --
obs0.166 666777 95.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.404→85.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32583 62785 277 0 95645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006103848
X-RAY DIFFRACTIONf_angle_d1.078154926
X-RAY DIFFRACTIONf_dihedral_angle_d13.82747849
X-RAY DIFFRACTIONf_chiral_restr0.05719570
X-RAY DIFFRACTIONf_plane_restr0.0069101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.404-2.43080.31941910.27715697X-RAY DIFFRACTION69
2.4308-2.45940.3151620.256916850X-RAY DIFFRACTION73
2.4594-2.48940.31091860.250217611X-RAY DIFFRACTION77
2.4894-2.52090.27191870.249418432X-RAY DIFFRACTION80
2.5209-2.55410.29632040.248919386X-RAY DIFFRACTION85
2.5541-2.58910.31052170.248220385X-RAY DIFFRACTION89
2.5891-2.62610.31532280.246321533X-RAY DIFFRACTION94
2.6261-2.66530.31182250.239122653X-RAY DIFFRACTION99
2.6653-2.7070.26882210.23422944X-RAY DIFFRACTION100
2.707-2.75130.28972430.233722969X-RAY DIFFRACTION100
2.7513-2.79880.29512280.225522924X-RAY DIFFRACTION100
2.7988-2.84970.24072300.224122954X-RAY DIFFRACTION100
2.8497-2.90450.29842050.218123001X-RAY DIFFRACTION100
2.9045-2.96380.26342120.214322986X-RAY DIFFRACTION100
2.9638-3.02820.26192220.207422957X-RAY DIFFRACTION100
3.0282-3.09870.23222430.196522938X-RAY DIFFRACTION100
3.0987-3.17620.21472460.18322929X-RAY DIFFRACTION100
3.1762-3.2620.22032320.175623001X-RAY DIFFRACTION100
3.262-3.3580.21862210.166822988X-RAY DIFFRACTION100
3.358-3.46640.21292200.161223041X-RAY DIFFRACTION100
3.4664-3.59030.20332500.151822975X-RAY DIFFRACTION100
3.5903-3.73410.17992200.140523062X-RAY DIFFRACTION100
3.7341-3.9040.16062230.134323077X-RAY DIFFRACTION100
3.904-4.10980.17252180.128422997X-RAY DIFFRACTION100
4.1098-4.36730.16522640.126323150X-RAY DIFFRACTION100
4.3673-4.70450.16222200.121923168X-RAY DIFFRACTION100
4.7045-5.17790.14632520.119623071X-RAY DIFFRACTION100
5.1779-5.9270.15382440.122323266X-RAY DIFFRACTION100
5.927-7.46670.18622150.140623371X-RAY DIFFRACTION100
7.4667-85.53170.18222430.167323789X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more