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- PDB-3oto: Crystal Structure of the 30S ribosomal subunit from a KsgA mutant... -

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Basic information

Entry
Database: PDB / ID: 3oto
TitleCrystal Structure of the 30S ribosomal subunit from a KsgA mutant of Thermus thermophilus (HB8)
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S rRNA
KeywordsRIBOSOME / 30S ribosomal subunit / KsgA Knock-out / Post transcriptional rRNA modification / Antibiotic resistance / Decoding / decoding of genetic code / tRNA / mRNA
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain ...S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Ribosomal protein S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / S15/NS1, RNA-binding / Helix hairpin bin / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, type Z / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S14/S29 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Few Secondary Structures / Irregular / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Nucleotidyltransferase; domain 5 / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Helix Hairpins / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S19/S15
Similarity search - Domain/homology
: / : / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...: / : / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS5 / 30S ribosomal protein Thx / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å
AuthorsDemirci, H. / Murphy IV, F. / Belardinelli, R. / Kelley, A.C. / Ramakrishnan, V. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
CitationJournal: Rna / Year: 2010
Title: Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function.
Authors: Demirci, H. / Murphy, F. / Belardinelli, R. / Kelley, A.C. / Ramakrishnan, V. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
History
DepositionSep 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA
B: 30S RIBOSOMAL PROTEIN S2
C: 30S RIBOSOMAL PROTEIN S3
D: 30S RIBOSOMAL PROTEIN S4
E: 30S RIBOSOMAL PROTEIN S5
F: 30S RIBOSOMAL PROTEIN S6
G: 30S RIBOSOMAL PROTEIN S7
H: 30S RIBOSOMAL PROTEIN S8
I: 30S RIBOSOMAL PROTEIN S9
J: 30S RIBOSOMAL PROTEIN S10
K: 30S RIBOSOMAL PROTEIN S11
L: 30S RIBOSOMAL PROTEIN S12
M: 30S RIBOSOMAL PROTEIN S13
N: 30S RIBOSOMAL PROTEIN S14
O: 30S RIBOSOMAL PROTEIN S15
P: 30S RIBOSOMAL PROTEIN S16
Q: 30S RIBOSOMAL PROTEIN S17
R: 30S RIBOSOMAL PROTEIN S18
S: 30S RIBOSOMAL PROTEIN S19
T: 30S RIBOSOMAL PROTEIN S20
U: 30S RIBOSOMAL PROTEIN THX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)787,726159
Polymers783,66821
Non-polymers4,058138
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)402.089, 402.089, 173.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S rRNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 155076

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S RIBOSOMAL PROTEIN S2


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 13446664, UniProt: P80371*PLUS
#3: Protein 30S RIBOSOMAL PROTEIN S3


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 13446666, UniProt: P80372*PLUS
#4: Protein 30S RIBOSOMAL PROTEIN S4


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#5: Protein 30S RIBOSOMAL PROTEIN S5


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS
#6: Protein 30S RIBOSOMAL PROTEIN S6


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#7: Protein 30S RIBOSOMAL PROTEIN S7


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291
#8: Protein 30S RIBOSOMAL PROTEIN S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24319, UniProt: P0DOY9*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 13446668, UniProt: P80374*PLUS
#10: Protein 30S RIBOSOMAL PROTEIN S10


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80375, UniProt: Q5SHN7*PLUS
#11: Protein 30S RIBOSOMAL PROTEIN S11


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 4519421, UniProt: P80376*PLUS
#12: Protein 30S RIBOSOMAL PROTEIN S12


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17293, UniProt: Q5SHN3*PLUS
#13: Protein 30S RIBOSOMAL PROTEIN S13


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 4519420, UniProt: P80377*PLUS
#14: Protein 30S RIBOSOMAL PROTEIN S14


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24320, UniProt: P0DOY6*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80378, UniProt: Q5SJ76*PLUS
#16: Protein 30S RIBOSOMAL PROTEIN S16


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80379, UniProt: Q5SJH3*PLUS
#17: Protein 30S RIBOSOMAL PROTEIN S17


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24321, UniProt: P0DOY7*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80382, UniProt: Q5SLQ0*PLUS
#19: Protein 30S RIBOSOMAL PROTEIN S19


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#20: Protein 30S RIBOSOMAL PROTEIN S20


Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380
#21: Protein/peptide 30S RIBOSOMAL PROTEIN THX


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P32193, UniProt: Q5SIH3*PLUS

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Non-polymers , 3 types, 138 molecules

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


Mass: 24.305 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: Mg
#23: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: K
#24: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY
Sequence detailsTHE AUTHOR HAS INDICATED THAT THE UNIPROT ENTRY FOR CHAIN T HAS A SEQUENCING ERROR AND THAT VAL 41 IS CORRECT.

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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: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 6.5 / Details: pH 6.5, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2010
RadiationMonochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3.2 % / Av σ(I) over netI: 9.74 / Number: 476713 / Rmerge(I) obs: 0.132 / Χ2: 1.39 / D res high: 3.7 Å / D res low: 30 Å / Num. obs: 148472 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
9.933091.610.0722.0963.1
7.939.9395.210.0751.9623.1
6.947.9397.610.081.7873.1
6.316.9498.310.11.7823.1
5.866.3198.810.1131.6913.2
5.525.8699.110.1171.6113.2
5.245.5299.210.1231.4833.2
5.025.2499.310.1331.4473.2
4.825.0299.310.1451.3533.3
4.664.8299.310.1621.3143.2
4.514.6699.210.181.2633.3
4.394.5199.210.2091.1923.3
4.274.3999.210.2351.1763.3
4.174.279910.2791.1083.3
4.074.1798.810.3231.1533.3
3.994.0798.710.3771.143.3
3.913.9998.610.4211.1863.3
3.833.9198.210.4621.1033.2
3.763.8397.710.551.0993.2
3.73.7697.310.5891.0963.1
ReflectionResolution: 3.69→30 Å / Num. obs: 148472 / % possible obs: 98.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.132 / Χ2: 1.395 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.69-3.763.10.5891.872281.09697.3
3.76-3.833.20.5572941.09997.7
3.83-3.913.20.46273531.10398.2
3.91-3.993.30.42173801.18698.6
3.99-4.073.30.37773981.1498.7
4.07-4.173.30.32373981.15398.8
4.17-4.273.30.27974161.10899
4.27-4.393.30.23574691.17699.2
4.39-4.513.30.20974531.19299.2
4.51-4.663.30.1874331.26399.2
4.66-4.823.20.16274891.31499.3
4.82-5.023.30.14574601.35399.3
5.02-5.243.20.13375181.44799.3
5.24-5.523.20.12374881.48399.2
5.52-5.863.20.11775071.61199.1
5.86-6.313.20.11375051.69198.8
6.31-6.943.10.175091.78298.3
6.94-7.933.10.0874791.78797.6
7.93-9.933.10.07573571.96295.2
9.93-303.10.07273382.09691.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQE

2vqe


Resolution: 3.69→29.842 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8534 / SU ML: 0.37 / σ(F): 0 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 7073 5.04 %
Rwork0.1728 --
obs0.1757 140210 92.66 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.448 Å2 / ksol: 0.223 e/Å3
Displacement parametersBiso max: 403.91 Å2 / Biso mean: 127.0008 Å2 / Biso min: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1--12.5355 Å2-0 Å20 Å2
2---12.5355 Å20 Å2
3---25.0709 Å2
Refinement stepCycle: LAST / Resolution: 3.69→29.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19126 32511 138 0 51775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00555830
X-RAY DIFFRACTIONf_angle_d0.75982876
X-RAY DIFFRACTIONf_chiral_restr0.07310405
X-RAY DIFFRACTIONf_plane_restr0.0044897
X-RAY DIFFRACTIONf_dihedral_angle_d17.60425857
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.69-3.73180.32412010.26853685388679
3.7318-3.77560.34362080.25813910411882
3.7756-3.82160.31772020.24423914411683
3.8216-3.86990.29192190.23034009422885
3.8699-3.92070.26522080.21714117432587
3.9207-3.97430.25992220.21014150437288
3.9743-4.03090.27512630.21694191445489
4.0309-4.09090.26392480.21284201444989
4.0909-4.15470.27122500.19914214446490
4.1547-4.22260.24661960.18824402459892
4.2226-4.29520.24912050.16634404460992
4.2952-4.37310.22392480.16354416466493
4.3731-4.45690.23672320.16444483471594
4.4569-4.54760.21392540.15784514476895
4.5476-4.64610.2062460.15744512475895
4.6461-4.75380.23742210.15234613483496
4.7538-4.87220.20412580.14774601485996
4.8722-5.00330.22252270.13934618484597
5.0033-5.14980.20092510.13984632488397
5.1498-5.31520.21292360.13784655489198
5.3152-5.5040.19752470.13054686493398
5.504-5.72290.20012640.13774690495498
5.7229-5.98140.19912410.13794739498098
5.9814-6.29390.20552710.14284667493898
6.2939-6.68410.21662300.14714744497498
6.6841-7.19350.2132440.14314738498298
7.1935-7.90520.19442340.14224741497597
7.9052-9.02130.21262550.16894644489995
9.0213-11.26340.24242440.17894657490194
11.2634-29.84310.24712480.2274590483890
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2128-0.0468-0.06950.3530.0670.22170.01520.0435-0.12880.18560.04430.12930.14430.044-0.04250.25930.03890.08060.16140.02720.2863143.025682.9878-12.4817
21.5787-0.34970.27810.0289-0.01510.09910.0579-1.05730.59540.00090.1312-0.18950.0144-0.017-0.17940.2151-0.13170.03751.1975-0.64670.7753222.1687128.21599.9025
30.2314-0.0206-0.35450.1278-0.11860.4269-0.1097-0.1192-0.314-0.03250.1372-0.33090.16070.19650.00910.36380.1286-0.00630.37970.05220.5973165.211470.9249-25.4416
40.50930.64370.03281.15510.36830.37690.1045-0.02640.3686-0.66970.32190.0419-0.5030.0459-0.36920.6781-0.11250.42180.2768-0.14040.7221164.6866157.8256-17.6023
50.3183-0.18540.39090.1602-0.10310.8063-0.1796-1.08050.25150.0190.4123-0.0301-0.0004-0.4525-0.11710.21740.06790.02042.3012-0.76090.4138197.7936135.186327.0948
60.42660.1929-0.00310.4482-0.02580.02050.0431-0.15880.03280.77050.0405-0.1381-0.08790.0672-0.09560.69010.20590.32480.0862-0.2355-0.4546141.5594108.409732.3771
70.41570.1776-0.13090.33450.31860.68250.2461-0.24440.15160.18530.00470.03760.0720.3195-0.21390.2889-0.06320.12060.3688-0.16960.2289155.6932124.56480.4871
80.49090.005-0.30650.11020.03680.2831-0.29740.42670.0582-0.22110.0028-0.00650.14240.08390.28631.04760.14190.0011.3942-0.03130.3785173.2907116.3009-87.7854
90.93150.15210.64370.3920.2010.44390.2970.56261.2450.0255-0.22490.17090.05780.0707-0.08220.6869-0.01090.33270.98790.06681.4204235.7985137.4501-31.1272
100.40150.0775-0.14020.1917-0.11980.3593-0.02360.01250.12880.02770.05170.2080.15280.0846-0.01670.35040.08560.09710.33260.09070.3347133.741124.1517-23.6094
110.1957-0.11220.0740.12160.00980.076-0.0184-0.12550.80750.00940.1265-0.08020.01790.1162-0.11020.4063-0.20730.15430.7567-0.73052.1845235.1824157.7259-6.5403
120.018-0.11050.11460.4989-0.03380.5806-0.4647-0.55560.6610.00330.2019-0.3393-0.0334-0.64790.26750.78140.1032-0.11161.9814-1.23131.7936221.5359153.752326.0262
130.7677-0.062-0.40890.0920.03420.2147-0.07540.24930.28410.00540.0723-0.11460.0712-0.1305-0.02580.49380.04330.14730.58880.03730.6638210.399119.051-64.426
140.2587-0.1104-0.20260.4751-0.18180.3174-0.1165-0.00990.03010.20120.0131-0.0631-0.0349-0.07380.05510.31180.173-0.04730.28160.0120.1932168.165980.28175.6513
150.0801-0.1085-0.17020.26280.02570.76040.2874-0.49380.4321-0.1634-0.0301-0.00380.08690.4069-0.23950.59030.2128-0.1271.3907-0.35951.2084263.5703112.06712.1967
160.1760.2557-0.23880.4944-0.32180.3595-0.2248-0.46660.27320.0327-0.3432-0.0703-0.0471-0.0610.40730.65410.0345-0.20742.0302-0.51690.8891219.5555125.956326.2799
170.6938-0.0171-0.04230.88820.4470.22430.16220.4372-0.0264-0.44640.17670.030.1590.4-0.27850.38510.015-0.13730.59470.02840.0527141.2906103.1235-64.1592
180.92090.7117-0.07020.6308-0.12460.12990.4995-0.03380.88940.3111-0.12990.70190.0431-0.0249-0.30710.7936-0.09710.45080.34440.00050.9592108.890877.620212.7988
190.14540.14990.17090.49560.02740.1828-0.0424-0.0732-0.0213-0.01540.12130.17720.0285-0.1707-0.11510.3937-0.0776-0.00270.44040.14060.5489125.882583.7347-38.0322
200.5125-0.11720.23930.1020.06481.11330.216-0.0490.1021-0.0863-0.1184-0.06980.1195-0.3998-0.05070.5150.09730.12040.68640.06180.4631180.1351129.5933-69.0458
210.3051-0.1398-0.04720.08-0.02010.1653-0.3501-0.8090.05880.00890.0716-0.041-0.0526-0.1570.17591.15640.1169-0.41552.25350.1181.3248248.842297.9930.0531
220.0460.00950.03710.28140.12010.23250.0607-0.01460.05480.18940.29450.44610.2033-0.0373-0.25150.6811-0.15730.13540.47550.2460.9555105.138444.7744-24.2175
230.03670.0235-0.01090.0156-0.00440.00370.0378-0.1195-0.00870.0059-0.07410.1152-0.01550.0740.02051.1787-0.0587-0.1141.5874-0.67021.6962250.9303129.31367.1849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 5:920A5 - 920
2X-RAY DIFFRACTION2chain A and resseq 921:1400A921 - 1400
3X-RAY DIFFRACTION3chain A and resseq 1401:1544A1401 - 1544
4X-RAY DIFFRACTION4chain B and resseq 6:241B6 - 241
5X-RAY DIFFRACTION5chain C and resseq 2:208C2 - 208
6X-RAY DIFFRACTION6chain D and resseq 2:209D2 - 209
7X-RAY DIFFRACTION7chain E and resseq 5:155E5 - 155
8X-RAY DIFFRACTION8chain F and resseq 1:101F1 - 101
9X-RAY DIFFRACTION9chain G and resseq 2:156G2 - 156
10X-RAY DIFFRACTION10chain H and resseq 1:138H1 - 138
11X-RAY DIFFRACTION11chain I and resseq 2:128I2 - 128
12X-RAY DIFFRACTION12chain J and resseq 3:101J3 - 101
13X-RAY DIFFRACTION13chain K and resseq 11:129K11 - 129
14X-RAY DIFFRACTION14chain L and resseq 5:129L5 - 129
15X-RAY DIFFRACTION15chain M and resseq 2:126M2 - 126
16X-RAY DIFFRACTION16chain N and resseq 2:61N2 - 61
17X-RAY DIFFRACTION17chain O and resseq 2:89O2 - 89
18X-RAY DIFFRACTION18chain P and resseq 1:84P1 - 84
19X-RAY DIFFRACTION19chain Q and resseq 2:105Q2 - 105
20X-RAY DIFFRACTION20chain R and resseq 16:88R16 - 88
21X-RAY DIFFRACTION21chain S and resseq 2:82S2 - 82
22X-RAY DIFFRACTION22chain T and resseq 8:106T8 - 106
23X-RAY DIFFRACTION23chain U and resseq 2:26U2 - 26

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