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- PDB-1m1k: Co-crystal structure of azithromycin bound to the 50S ribosomal s... -

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Basic information

Entry
Database: PDB / ID: 1m1k
TitleCo-crystal structure of azithromycin bound to the 50S ribosomal subunit of Haloarcula marismortui
Components
  • (RIBOSOMAL PROTEIN ...) x 28
  • 23S RRNA23S ribosomal RNA
  • 5S RRNA5S ribosomal RNA
KeywordsRIBOSOME / 50S / azithromycin / macrolide / Haloarcula
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleotide binding / DNA repair / 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 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / 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 L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Helix Hairpins - #310 / 50S ribosomal protein L10, archaea / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal protein L19e, archaeal / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / 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 L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal protein L7Ae, archaea / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Ribosomal protein L24e / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / N-terminal domain of TfIIb / Helix-hairpin-helix domain / 50S ribosomal protein L10, insertion domain superfamily / Translation factors / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L31e, conserved site / Ribosomal protein L37ae / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L32e, conserved site / RRM (RNA recognition motif) domain / Ribosomal protein L6, conserved site-2 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L39e, conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily
Similarity search - Domain/homology
: / : / AZITHROMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 ...: / : / AZITHROMYCIN / : / 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: 3.2 Å
AuthorsHansen, J.L. / Ippolito, J.A. / Ban, N. / Nissen, P. / Moore, P.B. / Steitz, T.A.
CitationJournal: 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.
History
DepositionJun 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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.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)1,458,904263
Polymers1,451,91430
Non-polymers6,990233
Water142,0487885
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.751, 301.566, 574.436
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 / 23S ribosomal RNA


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 / 5S ribosomal RNA


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 / 60S 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 / 60S 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 / Ribosome / 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 / Ribosome


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 / 60S 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 / Ribosome


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 / Ribosome / 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 / Ribosome / 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 / Ribosome / 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 / 60S 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 / Ribosome / 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 / Ribosome / 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 / Ribosome / 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 / Ribosome


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 / Ribosome / 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 / Ribosome / 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 / Ribosome / 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, 8118 molecules

#31: Chemical ChemComp-ZIT / AZITHROMYCIN / Azithromycin


Mass: 748.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H72N2O12 / Comment: medication, antibiotic*YM
#32: Chemical...
ChemComp-MG / MAGNESIUM ION


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


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


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


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#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 / Water


Mass: 18.015 Da / Num. of mol.: 7885 / 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: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 6K, NaCl, EG, NH4+, MgCl2,, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 281K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2NaClSodium chloride11
3EG11
4NH4+11
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 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 23, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 366469 / Num. obs: 366469 / % possible obs: 0.99 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 10
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2 / Num. unique all: 30076 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 90.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.192
Reflection shell
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JJ2

1jj2


Resolution: 3.2→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2721 1 %RANDOM
Rwork0.214 ---
all0.214 ---
obs0.214 276945 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.671 Å2 / ksol: 0.273835 e/Å3
Displacement parametersBiso mean: 63 Å2
Baniso -1Baniso -2Baniso -3
1-22.92 Å20 Å20 Å2
2---10.26 Å20 Å2
3----12.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28801 61617 284 7885 98587
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.52
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it1.372
X-RAY DIFFRACTIONc_scangle_it2.162.5
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.305 258 1.1 %
Rwork0.307 23803 -
obs--80.3 %
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 DIFFRACTION5zit_best_closer_to_xray_adjust_dihedrals.parzit_best.top
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.5
LS refinement shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å

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