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- PDB-1ffk: CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA ... -

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Basic information

Entry
Database: PDB / ID: 1ffk
TitleCRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI AT 2.4 ANGSTROM RESOLUTION
Components
  • (RIBOSOMAL PROTEIN ...) x 27
  • 23S RRNA
  • 5S RRNA
KeywordsRIBOSOME / ribosome assembly / RNA-RNA / protein-RNA / protein-protein
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, 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 L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, 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 L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / : / Ribosomal protein L7Ae, archaea / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / 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 L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L32e / Ribosomal protein L37ae/L37e / Ribosomal protein L32e superfamily / Ribosomal protein L32 / Ribosomal_L32e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 ...: / : / : / 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 uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / 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 / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBan, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A.
Citation
Journal: 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.
#1: Journal: Science / Year: 2000
Title: The structural basis of ribosome activity in peptide bond synthesis
Authors: Nissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.A.
#2: Journal: Nature / Year: 1999
Title: Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit
Authors: Ban, N. / Nissen, P. / Hansen, J. / Capel, M. / Moore, P.B. / Steitz, T.A.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: A 9 A resolution X-ray crystallographic map of the large ribosomal subunit
Authors: Ban, N. / Freeborn, B. / Nissen, P. / Penczek, P. / Grasucci, R.A. / Sweet, R. / Frank, J. / Moore, P.B. / Steitz, T.A.
History
DepositionJul 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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_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_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_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S RRNA
9: 5S RRNA
A: RIBOSOMAL PROTEIN L2
B: RIBOSOMAL PROTEIN L3
C: RIBOSOMAL PROTEIN L4
D: RIBOSOMAL PROTEIN L5
E: RIBOSOMAL PROTEIN L7AE
F: RIBOSOMAL PROTEIN L10E
G: RIBOSOMAL PROTEIN L13
H: RIBOSOMAL PROTEIN L14
I: RIBOSOMAL PROTEIN L15E
J: RIBOSOMAL PROTEIN L15
K: RIBOSOMAL PROTEIN L18
L: RIBOSOMAL PROTEIN L18E
M: RIBOSOMAL PROTEIN L19
N: RIBOSOMAL PROTEIN L21E
O: RIBOSOMAL PROTEIN L22
P: RIBOSOMAL PROTEIN L23
Q: RIBOSOMAL PROTEIN L24
R: RIBOSOMAL PROTEIN L24E
S: RIBOSOMAL PROTEIN L29
T: RIBOSOMAL PROTEIN L30
U: RIBOSOMAL PROTEIN L31E
V: RIBOSOMAL PROTEIN L32E
W: RIBOSOMAL PROTEIN L37AE
X: RIBOSOMAL PROTEIN L37E
Y: RIBOSOMAL PROTEIN L39E
Z: RIBOSOMAL PROTEIN L44E
1: RIBOSOMAL PROTEIN L6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,404,95836
Polymers1,404,42129
Non-polymers5377
Water1086
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
Cell settingorthorhombic
Space group name H-MC2221

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Components

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RNA chain , 2 types, 2 molecules 09

#1: RNA chain 23S RRNA


Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779
#2: RNA chain 5S RRNA


Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779

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RIBOSOMAL PROTEIN ... , 27 types, 27 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ1

#3: Protein RIBOSOMAL PROTEIN L2 / 50S RIBOSOMAL PROTEIN L2P / HMAL2 / HL4 / Coordinate model: Cα atoms only


Mass: 25237.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#4: Protein RIBOSOMAL PROTEIN L3 / 50S RIBOSOMAL PROTEIN L3P / HMAL3 / HL1 / Coordinate model: Cα atoms only


Mass: 37223.176 Da / Num. of mol.: 1 / Mutation: GLU67 DELETION, TYR312 INSERTION / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#5: Protein RIBOSOMAL PROTEIN L4 / 50S RIBOSOMAL PROTEIN L4E / HMAL4 / HL6 / Coordinate model: Cα atoms only


Mass: 26443.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#6: Protein RIBOSOMAL PROTEIN L5 / 50S RIBOSOMAL PROTEIN L5P / HMAL5 / HL13 / Coordinate model: Cα atoms only


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#7: Protein RIBOSOMAL PROTEIN L7AE / 30S RIBOSOMAL PROTEIN HS6 / Coordinate model: Cα atoms only


Mass: 12600.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#8: Protein RIBOSOMAL PROTEIN L10E / Coordinate model: Cα atoms only


Mass: 17231.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617*PLUS
#9: Protein RIBOSOMAL PROTEIN L13 / 50S RIBOSOMAL PROTEIN L13P / HMAL13 / Coordinate model: Cα atoms only


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P29198
#10: Protein RIBOSOMAL PROTEIN L14 / 50S RIBOSOMAL PROTEIN L14P / HMAL14 / HL27 / Coordinate model: Cα atoms only


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#11: Protein RIBOSOMAL PROTEIN L15E / Coordinate model: Cα atoms only


Mass: 23372.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618*PLUS
#12: Protein RIBOSOMAL PROTEIN L15 / 50S RIBOSOMAL PROTEIN L15P / HMAL15 / HL9 / Coordinate model: Cα atoms only


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#13: Protein RIBOSOMAL PROTEIN L18 / 50S RIBOSOMAL PROTEIN L18P / HMAL18 / HL12 / Coordinate model: Cα atoms only


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#14: Protein RIBOSOMAL PROTEIN L18E / 50S RIBOSOMAL PROTEIN L18E / HL29 / L19 / Coordinate model: Cα atoms only


Mass: 12307.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#15: Protein RIBOSOMAL PROTEIN L19 / 50S RIBOSOMAL PROTEIN L19E / HMAL19 / HL24 / Coordinate model: Cα atoms only


Mass: 16631.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#16: Protein RIBOSOMAL PROTEIN L21E / 50S RIBOSOMAL PROTEIN L21E / HL31 / Coordinate model: Cα atoms only


Mass: 10436.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#17: Protein RIBOSOMAL PROTEIN L22 / 50S RIBOSOMAL PROTEIN L22P / HMAL22 / HL23 / Coordinate model: Cα atoms only


Mass: 16835.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#18: Protein RIBOSOMAL PROTEIN L23 / 50S RIBOSOMAL PROTEIN L23P / HMAL23 / HL25 / L21 / Coordinate model: Cα atoms only


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#19: Protein RIBOSOMAL PROTEIN L24 / 50S RIBOSOMAL PROTEIN L24P / HMAL24 / HL16 / HL15 / Coordinate model: Cα atoms only


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#20: Protein RIBOSOMAL PROTEIN L24E / 50S RIBOSOMAL PROTEIN L24E / HL21/HL22 / Coordinate model: Cα atoms only


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#21: Protein RIBOSOMAL PROTEIN L29 / 50S RIBOSOMAL PROTEIN L29P / HMAL29 / HL33 / Coordinate model: Cα atoms only


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#22: Protein RIBOSOMAL PROTEIN L30 / 50S RIBOSOMAL PROTEIN L30P / HMAL30 / HL20 / HL16 / Coordinate model: Cα atoms only


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#23: Protein RIBOSOMAL PROTEIN L31E / 50S RIBOSOMAL PROTEIN L31E / L34 / HL30 / Coordinate model: Cα atoms only


Mass: 10253.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#24: Protein RIBOSOMAL PROTEIN L32E / 50S RIBOSOMAL PROTEIN L32E / HL5 / Coordinate model: Cα atoms only


Mass: 16223.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12736
#25: Protein RIBOSOMAL PROTEIN L37AE / Coordinate model: Cα atoms only


Mass: 8085.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619*PLUS
#26: Protein RIBOSOMAL PROTEIN L37E / 50S RIBOSOMAL PROTEIN L37E / L35E / Coordinate model: Cα atoms only


Mass: 6199.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#27: Protein/peptide RIBOSOMAL PROTEIN L39E / 50S RIBOSOMAL PROTEINS L39E / HL39E / HL46E / Coordinate model: Cα atoms only


Mass: 5994.880 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22452
#28: Protein RIBOSOMAL PROTEIN L44E / 50S RIBOSOMAL PROTEIN L44E / LA / HLA / Coordinate model: Cα atoms only


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32411
#29: Protein RIBOSOMAL PROTEIN L6 / 50S RIBOSOMAL PROTEIN L6P / HMAL6 / HL10 / Coordinate model: Cα atoms only


Mass: 19830.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135

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Non-polymers , 4 types, 13 molecules

#30: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#31: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#32: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#33: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 292 K / Method: backextraction, vapor diffusion / pH: 5.8
Details: PEG 6000, KCl, NH4Cl, MgCl2, CdCl2, potassium acetate, Tris-MES, pH 5.8, backextraction, vapor diffusion, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2NH4Cl11
3MgCl211
4CdCl211
5potassium acetate11
6Tris-MES11
7PEG 600011
8PEG 600012
Crystal grow
*PLUS
pH: 7.1 / Method: back-extraction, vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 M1reservoirKCl
20.5 M1reservoirNH4Cl
3100 mMKacetate1reservoir
430 mM1reservoirMgCl2
57 %PEG60001reservoir
615 mMTris1reservoir
715 mMMES1reservoir
81 mM1reservoirCdCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X2510.9
SYNCHROTRONAPS 19-ID21
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEFeb 25, 2000
CUSTOM-MADE2CCDApr 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
211
ReflectionResolution: 2.4→90 Å / Num. all: 666819 / Num. obs: 666819 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.691 / Num. unique all: 50941 / % possible all: 73.5
Reflection
*PLUS
Num. measured all: 6089802
Reflection shell
*PLUS
% possible obs: 71 % / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
TNT& CNSrefinement
CNSphasing
RefinementResolution: 2.4→90 Å / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: Engh & Huber, Parkinson et al.
Details: Real-space refinement in TNT against experimental map followed by phase-restrained refinement in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 5661 1 %random
Rwork0.252 ---
all-666819 --
obs-577304 82.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.633 Å20 Å20 Å2
2--1 Å20 Å2
3---4.633 Å2
Refinement stepCycle: LAST / Resolution: 2.4→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 60612 7 6 64281
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006422
X-RAY DIFFRACTIONc_angle_deg1.19599
X-RAY DIFFRACTIONc_torsion_deg28.81935
X-RAY DIFFRACTIONc_torsion_impr_deg1.6862
Software
*PLUS
Name: 'TNT & CNS' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 90 Å / σ(F): 2 / % reflection Rfree: 1 % / Rfactor obs: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg28.8
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_improper_angle_deg1.68

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