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- PDB-1k8a: Co-crystal structure of Carbomycin A bound to the 50S ribosomal s... -

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Basic information

Entry
Database: PDB / ID: 1k8a
TitleCo-crystal structure of Carbomycin A bound to the 50S ribosomal subunit of Haloarcula marismortui
Components
  • (RIBOSOMAL PROTEIN ...) x 28
  • 23S RRNA
  • 5S RRNA
KeywordsRIBOSOME / antibiotic / carbomycin A / macrolide
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
CARBOMYCIN A / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 ...CARBOMYCIN A / : / : / : / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHansen, J.L. / Ippolito, J.A. / Ban, N. / Nissen, P. / Moore, P.B. / Steitz, T.
Citation
Journal: Mol.Cell / Year: 2002
Title: The structures of four macrolide antibiotics bound to the large ribosomal subunit.
Authors: Hansen, J.L. / Ippolito, J.A. / Ban, N. / Nissen, P. / Moore, P.B. / Steitz, T.A.
#1: 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.
#2: 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.
History
DepositionOct 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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_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_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
A: 23S RRNA
B: 5S RRNA
C: RIBOSOMAL PROTEIN L2
D: RIBOSOMAL PROTEIN L3
E: RIBOSOMAL PROTEIN L4
F: RIBOSOMAL PROTEIN L5
G: RIBOSOMAL PROTEIN L6
H: RIBOSOMAL PROTEIN L7AE
I: RIBOSOMAL PROTEIN L10
J: RIBOSOMAL PROTEIN L10E
K: RIBOSOMAL PROTEIN L13
L: RIBOSOMAL PROTEIN L14
M: RIBOSOMAL PROTEIN L15
N: RIBOSOMAL PROTEIN L15E
O: RIBOSOMAL PROTEIN L18
P: RIBOSOMAL PROTEIN L18E
Q: RIBOSOMAL PROTEIN L19E
R: RIBOSOMAL PROTEIN L21E
S: RIBOSOMAL PROTEIN L22
T: RIBOSOMAL PROTEIN L23
U: RIBOSOMAL PROTEIN L24
V: RIBOSOMAL PROTEIN L24E
W: RIBOSOMAL PROTEIN L29
X: RIBOSOMAL PROTEIN L30
Y: RIBOSOMAL PROTEIN L31E
Z: RIBOSOMAL PROTEIN L32E
1: RIBOSOMAL PROTEIN L37Ae
2: RIBOSOMAL PROTEIN L37E
3: RIBOSOMAL PROTEIN L39E
4: RIBOSOMAL PROTEIN L44E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,459,051264
Polymers1,451,91430
Non-polymers7,137234
Water141,4187850
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.902, 300.474, 575.176
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 , 2 types, 2 molecules AB

#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

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RIBOSOMAL PROTEIN ... , 28 types, 28 molecules CDEFGHIJKLMNOPQRSTUVWXYZ1234

#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: Protein RIBOSOMAL PROTEIN L7AE / 50S 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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 , 7 types, 8084 molecules

#31: Chemical ChemComp-CAI / CARBOMYCIN A


Mass: 841.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H67NO16
#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 119 / Source method: obtained synthetically / Formula: Mg
#33: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 83 / Source method: obtained synthetically / Formula: Na
#34: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#35: Chemical ChemComp-K / POTASSIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 7850 / 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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 6K, KCl, NH4Cl, KOAc MgCl2, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2KCl11
3NH4Cl11
4KOAC11
5MgCl211
Crystal grow
*PLUS
pH: 7.1 / Method: back-extraction, vapor diffusion / Details: Ban, N., (2000) Science, 289, 905.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.2 M1reservoirKCl
20.5 M1reservoirNH4Cl
3100 mMKacetate1reservoir
430 mM1reservoirMgCl2
57 %PEG60001reservoir
615 mMTris1reservoir
715 mMMES1reservoir
81 mM1reservoirCdCl2pH7.1

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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 27, 2000
RadiationMonochromator: Si 111 Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 370864 / Num. obs: 367880 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 14.2
Reflection shellResolution: 2.98→3.09 Å / Redundancy: 34384 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2 / Num. unique all: 36270 / Rsym value: 0.816 / % possible all: 94.8
Reflection
*PLUS
% possible obs: 93.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.132
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 80.2 % / Rmerge(I) obs: 0.68

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JJ2 native 50S subunit

1jj2


Resolution: 3→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 270687.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: RNA from CNS Brunger, Berman modified by Sjoerd Protein from CNS protein_rep.param Carbomycin A constructed from CSD files DMCLM10, NAVTAF, PVVBDM01, using xplo2d
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3311 1 %RANDOM same r-free set as 1JJ2
Rwork0.227 ---
all0.227 364257 --
obs0.227 339428 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.6577 Å2 / ksol: 0.291887 e/Å3
Displacement parametersBiso mean: 58.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.62 Å20 Å20 Å2
2---1.81 Å20 Å2
3----5.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28801 61617 292 7850 98560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.252
X-RAY DIFFRACTIONc_scangle_it22.5
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 286 1 %
Rwork0.348 28711 -
obs--80.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1RNA_JEFF.PARAM5RNA_JEFF.TOP5
X-RAY DIFFRACTION2PROTEIN_JEFF.PARAM3PROTEIN_TYM.TOP3
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION5CAR_LINK_TETRA.PARCAR_LINK_TETRA.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.6
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å

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