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- PDB-1kqs: The Haloarcula marismortui 50S Complexed with a Pretranslocationa... -

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Basic information

Entry
Database: PDB / ID: 1kqs
TitleThe Haloarcula marismortui 50S Complexed with a Pretranslocational Intermediate in Protein Synthesis
Components
  • (RIBOSOMAL PROTEIN ...) x 28
  • 23S RRNA
  • 5S RRNA
  • CC-Pmn-pcb
  • CCA
KeywordsRIBOSOME / RIBOSOME ASSEMBLY / RNA-RNA / PROTEIN-RNA / PROTEIN-PROTEIN / PROTEIN SYNTHESIS / PEPTIDYL TRANSFERASE
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
Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / Helix Hairpins - #310 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / 50S ribosomal protein L10, archaea / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L2; domain 3 / Ribosomal protein L2, 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 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L30; Chain: A, / SH3 type barrels. - #30 / : / Ribosomal protein L30/S12 / Ribosomal Protein L22; Chain A / Ribosomal protein L7Ae, archaea / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / : / N-terminal domain of TfIIb / Translation factors / Helix-hairpin-helix domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / RRM (RNA recognition motif) domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 60s Ribosomal Protein L30; Chain: A; / 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. / Single Sheet / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature.
Similarity search - Domain/homology
6-AMINOHEXANOIC ACID / BIOTIN / : / : / PHENYLALANINAL / PUROMYCIN-5'-MONOPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) ...6-AMINOHEXANOIC ACID / BIOTIN / : / : / PHENYLALANINAL / PUROMYCIN-5'-MONOPHOSPHATE / : / 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 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsSchmeing, T.M. / Seila, A.C. / Hansen, J.L. / Freeborn, B. / Soukup, J.K. / Scaringe, S.A. / Strobel, S.A. / Moore, P.B. / Steitz, T.A.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits.
Authors: Schmeing, T.M. / Seila, A.C. / Hansen, J.L. / Freeborn, B. / Soukup, J.K. / Scaringe, S.A. / Strobel, S.A. / Moore, P.B. / Steitz, T.A.
History
DepositionJan 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.pdbx_leaving_atom_flag / _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 / _struct_ref.pdbx_seq_one_letter_code / _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
3: CCA
4: CC-Pmn-pcb
A: RIBOSOMAL PROTEIN L2
B: RIBOSOMAL PROTEIN L3
C: RIBOSOMAL PROTEIN L4
D: RIBOSOMAL PROTEIN L5
E: RIBOSOMAL PROTEIN L6
F: RIBOSOMAL PROTEIN L7AE
G: RIBOSOMAL PROTEIN L10
H: RIBOSOMAL PROTEIN L10E
I: RIBOSOMAL PROTEIN L13
J: RIBOSOMAL PROTEIN L14
K: RIBOSOMAL PROTEIN L15
L: RIBOSOMAL PROTEIN L15E
M: RIBOSOMAL PROTEIN L18
N: RIBOSOMAL PROTEIN L18E
O: RIBOSOMAL PROTEIN L19E
P: RIBOSOMAL PROTEIN L21E
Q: RIBOSOMAL PROTEIN L22
R: RIBOSOMAL PROTEIN L23
S: RIBOSOMAL PROTEIN L24
T: RIBOSOMAL PROTEIN L24E
U: RIBOSOMAL PROTEIN L29
V: RIBOSOMAL PROTEIN L30
W: RIBOSOMAL PROTEIN L31E
X: RIBOSOMAL PROTEIN L32E
Y: RIBOSOMAL PROTEIN L37Ae
Z: RIBOSOMAL PROTEIN L37E
1: RIBOSOMAL PROTEIN L39E
2: RIBOSOMAL PROTEIN L44E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,460,691268
Polymers1,453,37432
Non-polymers7,317236
Water141,7967871
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.784, 300.349, 574.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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RNA chain , 4 types, 4 molecules 0934

#1: RNA chain 23S RRNA


Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779
#3: RNA chain CCA


Mass: 894.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase synthesis
#4: RNA chain CC-Pmn-pcb


Mass: 565.406 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Solid phase synthesis, followed by peptidyl transferase reaction.

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RIBOSOMAL PROTEIN ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ12

#5: Protein RIBOSOMAL PROTEIN L2 / 50S RIBOSOMAL PROTEIN L2P / HMAL2 / HL4


Mass: 25237.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#6: Protein RIBOSOMAL PROTEIN L3 / 50S RIBOSOMAL PROTEIN L3P / HMAL3 / HL1


Mass: 37265.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#7: Protein RIBOSOMAL PROTEIN L4 / 50S RIBOSOMAL PROTEIN L4E / HMAL4 / HL6


Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#8: Protein RIBOSOMAL PROTEIN L5 / 50S RIBOSOMAL PROTEIN L5P / HMAL5 / HL13


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#9: Protein RIBOSOMAL PROTEIN L6 / 50S RIBOSOMAL PROTEIN L6P / HMAL6 / HL10


Mass: 19830.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135
#10: Protein RIBOSOMAL PROTEIN L7AE / 30S RIBOSOMAL PROTEIN HS6


Mass: 12600.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#11: Protein RIBOSOMAL PROTEIN L10 / 50S RIBOSOMAL PROTEIN P0 / HMAL10 / L10E


Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825
#12: Protein RIBOSOMAL PROTEIN L10E


Mass: 18022.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617*PLUS
#13: Protein RIBOSOMAL PROTEIN L13 / 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) / References: UniProt: P29198
#14: Protein RIBOSOMAL PROTEIN L14 / 50S RIBOSOMAL PROTEIN L14P / HMAL14 / HL27


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#15: Protein RIBOSOMAL PROTEIN L15 / 50S RIBOSOMAL PROTEIN L15P / HMAL15 / HL9


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#16: Protein RIBOSOMAL PROTEIN L15E


Mass: 22856.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618*PLUS
#17: Protein RIBOSOMAL PROTEIN L18 / 50S RIBOSOMAL PROTEIN L18P / HMAL18 / HL12


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#18: Protein RIBOSOMAL PROTEIN L18E / 50S RIBOSOMAL PROTEIN L18E / HL29 / L19


Mass: 12307.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#19: Protein RIBOSOMAL PROTEIN L19E / 50S RIBOSOMAL PROTEIN L19E / HMAL19 / HL24


Mass: 16631.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#20: Protein RIBOSOMAL PROTEIN L21E / 50S RIBOSOMAL PROTEIN L21E / HL31


Mass: 10436.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#21: Protein RIBOSOMAL PROTEIN L22 / 50S RIBOSOMAL PROTEIN L22P / HMAL22 / HL23


Mass: 16835.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#22: Protein RIBOSOMAL PROTEIN L23 / 50S RIBOSOMAL PROTEIN L23P / HMAL23 / HL25 / L21


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#23: Protein RIBOSOMAL PROTEIN L24 / 50S RIBOSOMAL PROTEIN L24P / HMAL24 / HL16 / HL15


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#24: Protein RIBOSOMAL PROTEIN L24E / 50S RIBOSOMAL PROTEIN L24E / HL21/HL22


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#25: Protein RIBOSOMAL PROTEIN L29 / 50S RIBOSOMAL PROTEIN L29P / HMAL29 / HL33


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#26: Protein RIBOSOMAL PROTEIN L30 / 50S RIBOSOMAL PROTEIN L30P / HMAL30 / HL20 / HL16


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#27: Protein RIBOSOMAL PROTEIN L31E / 50S RIBOSOMAL PROTEIN L31E / L34 / HL30


Mass: 10253.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#28: Protein RIBOSOMAL PROTEIN L32E / 50S RIBOSOMAL PROTEIN L32E / HL5


Mass: 26324.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12736
#29: Protein RIBOSOMAL PROTEIN L37Ae


Mass: 8097.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619*PLUS
#30: Protein RIBOSOMAL PROTEIN L37E / 50S RIBOSOMAL PROTEIN L37E / L35E


Mass: 6199.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#31: Protein/peptide RIBOSOMAL PROTEIN L39E / 50S RIBOSOMAL PROTEINS L39E / HL39E / HL46E


Mass: 5844.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22452
#32: Protein RIBOSOMAL PROTEIN L44E / 50S RIBOSOMAL PROTEIN L44E / LA / HLA


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32411

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Non-polymers , 10 types, 8107 molecules

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


Mass: 24.305 Da / Num. of mol.: 117 / Source method: obtained synthetically / Formula: Mg
#34: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#35: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Na
#36: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#37: Chemical ChemComp-PPU / PUROMYCIN-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 551.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O8P
#38: Chemical ChemComp-PHA / PHENYLALANINAL


Type: L-peptide linking / Mass: 149.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO
#39: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#40: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#41: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 7871 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 6000, KCl, NH4Cl, MgCl2, CdCl2, POTASSIUM ACETATE, TRIS-MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2KCl11
3NH4Cl11
4MgCl211
5CdCl211
6POTASSIUM ACETATE11
7TRIS-MES11
Crystal grow
*PLUS
Method: unknown / Details: data unknown
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51
61
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.07→45 Å / Num. all: 2581688 / Num. obs: 2581688 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.07→3.15 Å / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 45 Å / Num. obs: 340617 / Redundancy: 7.6 % / Num. measured all: 2581688
Reflection shell
*PLUS
% possible obs: 99.7 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2202 3088 RANDOM
Rwork0.1728 --
all0.1732 328866 -
obs0.1732 316760 -
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28801 61713 303 7871 98688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.333
X-RAY DIFFRACTIONc_angle_d2.161
LS refinement shellResolution: 3.1→3.12 Å / Num. reflection Rfree: 57
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.1709 / Rfactor Rfree: 0.2205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.161
LS refinement shell
*PLUS
Highest resolution: 3.07 Å / Lowest resolution: 3.15 Å

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