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- PDB-5br8: Ambient-temperature crystal structure of 30S ribosomal subunit fr... -

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Basic information

Entry
Database: PDB / ID: 5br8
TitleAmbient-temperature crystal structure of 30S ribosomal subunit from Thermus thermophilus in complex with paromomycin
Components
  • (30S ribosomal protein ...) x 20
  • 16S ribosomal RNA
KeywordsRIBOSOME / 30S ribosomal subunit / Paromomycin / Ambient temperature / SFX / electrospinning
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / 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 S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Few Secondary Structures / Irregular / 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. / Ribosomal protein S2 signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / : / Ribosomal protein S5, N-terminal, conserved site
Similarity search - Domain/homology
PAROMOMYCIN / : / 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 ...PAROMOMYCIN / : / 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 uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSierra, R.G. / Gati, C. / Laksmono, H. / Dao, E.H. / Gul, S. / Fuller, F. / Kern, J. / Chatterjee, R. / Ibrahim, M. / Brewster, A. ...Sierra, R.G. / Gati, C. / Laksmono, H. / Dao, E.H. / Gul, S. / Fuller, F. / Kern, J. / Chatterjee, R. / Ibrahim, M. / Brewster, A. / Young, I.D. / Michels-Clark, T. / Aquila, A. / Mengning, L. / Hunter, M.S. / Koglin, J.E. / Boutet, S. / Junco, E.A. / Hayes, B. / Bogan, M.J. / Hampton, C.Y. / Puglisi, E.V. / Sauter, N.K. / Stan, C.A. / Zouni, A. / Yano, J. / Yachandra, V.K. / Soltis, S.M. / Puglisi, J.D. / DeMirci, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51266 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082545 United States
CitationJournal: To Be Published
Title: Ambient-temperature crystal structure of 30S ribosomal subunit from Thermus thermophilus in complex with paromomycin
Authors: Sierra, R.G. / Gati, C. / Laksmono, H. / Dao, E.H. / Gul, S. / Fuller, F. / Kern, J. / Chatterjee, R. / Ibrahim, M. / Brewster, A. / Young, I.D. / Michels-Clark, T. / Aquila, A. / Mengning, ...Authors: Sierra, R.G. / Gati, C. / Laksmono, H. / Dao, E.H. / Gul, S. / Fuller, F. / Kern, J. / Chatterjee, R. / Ibrahim, M. / Brewster, A. / Young, I.D. / Michels-Clark, T. / Aquila, A. / Mengning, L. / Hunter, M.S. / Koglin, J.E. / Boutet, S. / Junco, E.A. / Hayes, B. / Bogan, M.J. / Hampton, C.Y. / Puglisi, E.V. / Sauter, N.K. / Stan, C.A. / Zouni, A. / Yano, J. / Yachandra, V.K. / Soltis, S.M. / Puglisi, J.D. / DeMirci, H.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Structure summary
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Feb 12, 2025Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S ribosomal RNA
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 type Z
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)794,735316
Polymers783,93521
Non-polymers10,800295
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area104270 Å2
ΔGint-865 kcal/mol
Surface area270870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)401.300, 401.300, 176.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 ribosomal RNA


Mass: 494169.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382

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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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12


Mass: 14966.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

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Non-polymers , 4 types, 603 molecules

#22: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#23: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: Mg
#24: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#25: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.59 Å3/Da / Density % sol: 73.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPD

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.29 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 3.4→52.84 Å / Num. obs: 195895 / % possible obs: 100 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.29 / Net I/σ(I): 3
Reflection shellHighest resolution: 3.4 Å / Rmerge(I) obs: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DR2

4dr2


Resolution: 3.4→52.84 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1413 0.72 %
Rwork0.1928 --
obs0.1931 195895 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→52.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19143 32504 541 308 52496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00656417
X-RAY DIFFRACTIONf_angle_d0.85983597
X-RAY DIFFRACTIONf_dihedral_angle_d20.27726590
X-RAY DIFFRACTIONf_chiral_restr0.0410505
X-RAY DIFFRACTIONf_plane_restr0.0044897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.52150.3571390.311319216X-RAY DIFFRACTION100
3.5215-3.66250.29071400.27519229X-RAY DIFFRACTION100
3.6625-3.82910.31821410.24919273X-RAY DIFFRACTION100
3.8291-4.03090.28081390.216719286X-RAY DIFFRACTION100
4.0309-4.28340.22711410.199919347X-RAY DIFFRACTION100
4.2834-4.61390.22431410.182419392X-RAY DIFFRACTION100
4.6139-5.07790.21631410.166819425X-RAY DIFFRACTION100
5.0779-5.81190.22651410.162719466X-RAY DIFFRACTION100
5.8119-7.31920.18541440.166719666X-RAY DIFFRACTION100
7.3192-52.83580.2121460.175520182X-RAY DIFFRACTION100
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)
10.3476-0.1627-0.09130.3390.1010.26720.0464-0.11920.0883-0.02920.04780.013-0.0199-0.0361-0.09820.6272-0.1013-0.01610.6803-0.08030.9913-116.46656.152232.2927
20.61590.23910.02461.11630.05790.41350.0873-0.2739-0.09380.58180.0318-0.27850.19150.2203-0.10581.14010.1665-0.32520.796-0.1490.949-70.7711-23.167453.6399
30.3232-0.9759-0.4052.05440.60540.07850.12650.126-0.40690.0976-0.19790.67820.0261-0.18380.08530.8248-0.08010.00060.9039-0.08351.1882-130.863336.515619.3533
44.92696.1031-6.69197.6774-8.35449.1371-0.51570.5313-1.91440.9138-0.3470.52162.951-0.96180.79743.4343-0.52840.75071.5918-0.47332.3757-88.2565-3.83711.4353
57.7545-0.6646-2.1574.1513-2.25282.0509-0.21411.14-2.0221-0.81690.6677-1.0098-0.40721.2362-0.27590.7002-0.37870.09551.8097-0.39841.2197-43.07743.20868.4124
63.8124-1.16122.04872.2615-2.95494.6285-0.18030.8960.6946-0.0355-0.0552-0.4856-1.29321.16840.3930.6772-0.32480.16491.1773-0.18171.7448-44.13549.407517.023
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593.22590.7679-0.52450.5304-1.01872.5617-0.3291-0.5045-0.2833-0.19790.2823-0.57830.80080.2604-0.011.19340.2124-0.46820.7604-0.23951.4795-53.1298-26.510837.4664
604.89982.8935-4.87089.9584-0.12517.3850.51772.16051.2592-0.0095-0.90550.2806-0.5687-1.4790.41311.20530.3259-0.42781.0417-0.11680.8664-76.2-23.137637.3299
619.1139-7.29344.10478.3168-5.75236.38970.3266-0.68350.96520.4438-0.3675-0.77710.41471.55120.03131.24290.2406-0.48611.3705-0.36521.3926-37.1753-22.948170.3038
624.55512.8532-1.43483.2378-3.78327.0534-0.3419-1.60350.48810.5459-0.3472-0.9578-0.28241.30870.90341.36260.5448-0.88771.5171-0.26881.7948-33.8665-28.906966.7309
634.73921.0766-3.16096.7093.19864.48181.1645-0.3212-0.1919-0.8567-0.5910.04391.46650.523-0.59661.85490.3678-0.09930.7767-0.08351.9293-57.8692-25.83361.1192
645.3984-6.4626-0.33749.6391-1.09721.2825-0.9896-0.57721.6450.7456-0.1396-0.6581-0.32920.01381.13911.17840.1241-0.27831.0604-0.29660.8987-64.4003-18.887157.2018
656.99861.69811.69126.299-0.62446.7620.2933-1.6701-0.71650.3624-0.9481-0.9584-0.00661.14810.78541.58820.5825-0.92792.04190.0531.6459-30.3931-32.3273.9782
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897.74425.14284.1627.123.68214.89560.30770.16940.18690.1972-0.08390.2261-0.22810.5552-0.21540.8509-0.05950.28130.6196-0.03730.7246-96.054154.7824-21.7953
906.42871.1646-1.05978.92180.98976.76250.7374-0.48440.36852.0879-0.45770.2504-0.0887-0.2583-0.27990.8507-0.0582-0.02620.57680.08390.8244-98.341756.0452-11.509
916.06753.57114.06946.13846.9867.9560.3593-0.52680.67070.1657-0.70152.7016-0.9181-2.55710.28520.70350.13830.28271.07630.24491.5596-102.268868.4477-19.0195
922.19341.5204-0.79536.70650.10970.4148-0.059-0.9880.4650.2456-0.1892-1.3694-0.068-0.16060.2050.5722-0.0738-0.09670.8522-0.32761.0901-122.858482.11959.9209
930.9486-0.1762-2.28523.46590.11536.52760.4522-0.07020.39420.04020.1005-0.9323-0.5313-0.0508-0.60690.57620.02580.05380.7886-0.26571.2398-122.562384.547355.3672
941.9643-4.11584.3738.6463-9.20079.802-0.3481-0.04390.88411.1927-0.0776-1.1731-1.49171.22660.44530.9384-0.1839-0.09761.0243-0.58691.5586-113.342689.806865.2679
950.5391-1.439-0.74064.44322.90375.5168-0.09850.1340.2826-0.03650.8148-1.1824-0.52881.0597-0.69440.7052-0.22180.34190.6703-0.44441.7441-120.347298.444750.2733
963.92720.42551.58936.018-4.11654.9099-0.5059-0.94341.88771.7547-0.08170.9074-0.40840.06260.44590.82980.09540.09771.0899-0.57091.5985-124.553998.454561.197
978.75843.14114.61785.64653.24466.440.11451.01440.4089-0.20750.1391-0.5779-0.1140.498-0.21660.52180.0550.23740.50840.10150.8871-119.154879.28476.556
987.9585-5.70894.66116.957-3.73843.190.070.71010.34630.1479-0.1531-0.007-0.43620.09260.06880.63640.08560.2670.6446-0.03520.8514-115.338177.30849.2968
999.50867.5998-7.4816.0744-5.96326.013-0.60230.8579-0.9324-1.63670.7686-0.40251.1748-0.0258-0.10450.94980.0588-0.12770.8195-0.18860.6863-114.431361.13950.6369
1009.26116.65670.55684.98431.15313.2974-0.33660.3007-0.3216-0.0728-0.1078-2.09940.6441.82760.48670.9094-0.14550.18612.0714-0.6321.24-60.812418.9018-19.8204
1019.66610.7463.8284.6386-3.82915.24570.77740.5195-0.4944-0.5076-0.43720.86180.5119-0.3586-0.32571.340.0027-0.08131.4924-0.30471.7422-59.934524.4057-27.8091
1028.50631.340.32747.1303-2.71914.6993-0.40730.7353-1.50720.7547-0.5153-0.15551.2339-0.31470.83551.3191-0.19930.37690.8462-0.18151.3022-71.675627.1246-32.3639
1031.4031-1.25262.00274.7057-6.60039.3135-0.03921.0505-0.8002-1.34930.366-2.46731.04412.6688-0.44020.7143-0.1260.29060.9867-0.55071.4954-67.972418.1888-30.0177
1044.94936.92034.00969.80695.59073.2502-0.720.1903-1.12490.05751.0106-1.19861.23441.1047-0.28431.09330.03910.08560.9936-0.03051.0745-72.30412.9839-21.7179
1057.9984.91122.91378.37787.12219.42680.4363-0.11610.1450.59070.7753-0.3856-0.22280.952-1.14290.742-0.07710.20920.7562-0.10270.6555-73.692323.8171-22.6853
1064.25394.0787-0.76636.0069-2.79592.2030.90250.051-0.8152-0.8456-0.5586-0.08860.95191.4609-0.40791.02130.1968-0.11061.1115-0.25521.0163-75.13296.5327-26.7096
1078.3499-5.2194-6.15295.29196.16899.25270.21061.8020.9647-1.90830.01391.3565-2.7372-2.4259-0.26742.01110.0268-0.44311.0320.451.215-86.6333-52.409371.7378
1085.38795.2466-5.32975.2017-5.25575.31860.6518-2.07250.18641.9381-1.3320.3365-1.33661.0850.62491.947-0.24110.0381.1153-0.02030.8785-99.711-51.765186.6775
1099.2563-3.67077.29924.6195-6.06849.37820.352-0.02421.14682.1542-0.09033.2546-2.562-0.8159-0.34021.78920.2110.20840.8894-0.10551.5951-105.9139-46.572481.9206
1104.071.87545.84051.11312.55678.45330.4906-1.2656-0.42382.3593-0.3295-0.582-0.5640.0504-0.12562.32050.1764-0.1420.99790.09450.8055-94.9274-47.673773.8432
1119.1486-6.08984.04744.9074-4.57296.9643-0.2277-0.40590.09741.9562-0.47660.16120.3010.46110.76291.4452-0.1682-0.03150.89420.06560.8795-103.0663-50.404173.5672
1127.1081-6.0225.37419.0797-6.32194.8595-0.6013-1.059-0.89640.34141.8610.6049-0.6474-2.2388-1.23981.080.0625-0.05861.4550.08290.9181-102.4924-41.472362.71
1132.87032.2005-3.80821.6855-3.08988.2813-0.07090.08270.2787-0.0657-0.0539-0.10290.0077-0.40190.10160.50920.09430.13480.8446-0.20541.1941-157.778392.072325.1215
1143.35493.08382.18997.6704-1.31223.7168-0.3576-1.02280.3531-0.25220.4784-2.2307-0.21230.6445-0.10890.70560.06320.01331.05470.01561.3627-147.908894.328229.8823
1156.898-4.24096.73412.883-4.41937.90390.41210.40920.5424-0.6404-0.427-0.05751.75271.778-0.04021.10140.31770.47630.78020.01161.5324-147.458196.520313.4012
1169.94525.85567.89225.77544.836.2777-0.2766-0.5893-0.00460.3339-0.6274-0.3478-0.7402-0.01660.83871.1443-0.12280.03840.91170.35360.887-151.7715106.99455.8399
1175.54814.52225.66744.95645.44958.68581.5723-6.4361-1.86463.4846-2.6925-2.16771.82472.65171.18081.45380.0382-0.21341.77740.33551.3199-75.6146-51.97446.1005
1183.95080.2602-2.21545.36260.44143.1871-0.1651-0.12450.0835-0.03070.40310.22360.18460.1134-0.23611.3958-0.02590.13751.6358-0.14742.4048-70.5908-48.427747.8403
1197.96193.1642-1.35725.86081.80471.42410.7748-2.5669-3.23262.7351-0.2028-1.78692.61221.7915-0.54122.17020.3561-0.53721.50610.34551.6567-66.7422-54.280153.6141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1532)
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)
118X-RAY DIFFRACTION118chain 'U' and (resseq 9:15)
119X-RAY DIFFRACTION119chain 'U' and (resseq 16:25)

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