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- PDB-5wnp: Crystal Structure of 30S ribosomal subunit from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5wnp
TitleCrystal Structure of 30S ribosomal subunit from Thermus thermophilus
Components
  • (30S ribosomal protein ...) x 20
  • 16S Ribosomal RNA rRNA
  • RNA (5'-R(*AP*AP*AP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)-3')
KeywordsRIBOSOME / smFRET / mRNA methylation / translation / decoding
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
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 S7 / Ribosomal protein S7/S5 ...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 S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; 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 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / 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 S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / 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 / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Few Secondary Structures / Irregular / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S17, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18
Similarity search - Domain/homology
: / : / 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 ...: / : / 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 / 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 / FOURIER SYNTHESIS / Resolution: 3.3 Å
AuthorsDeMirci, 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)GM099687 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.
Authors: Choi, J. / Indrisiunaite, G. / DeMirci, H. / Ieong, K.W. / Wang, J. / Petrov, A. / Prabhakar, A. / Rechavi, G. / Dominissini, D. / He, C. / Ehrenberg, M. / Puglisi, J.D.
History
DepositionAug 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 21, 2018Group: Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_poly / entity_src_nat / pdbx_entity_src_syn
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity_name_com.entity_id / _entity_poly.type / _pdbx_entity_src_syn.entity_id
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 21, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns_shell ...pdbx_struct_conn_angle / reflns_shell / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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 / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S Ribosomal RNA 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 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
a: RNA (5'-R(*AP*AP*AP*UP*UP*U)-3')
b: RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)781,357300
Polymers774,21723
Non-polymers7,140277
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area108260 Å2
ΔGint-813 kcal/mol
Surface area277780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)400.000, 400.000, 173.000
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 , 3 types, 3 molecules Aab

#1: RNA chain 16S Ribosomal RNA rRNA


Mass: 494170.781 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
#22: RNA chain RNA (5'-R(*AP*AP*AP*UP*UP*U)-3')


Mass: 1861.157 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
#23: RNA chain RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)-3')


Mass: 4979.135 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S ribosomal protein S2 /


Mass: 27217.490 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: 22975.588 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: 24242.254 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: 16460.193 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: 17919.775 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: P0DOY9
#9: Protein 30S ribosomal protein S9 /


Mass: 14279.419 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: 11398.308 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: 12606.369 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: 13921.479 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: Q5SHN3
#13: Protein 30S ribosomal protein S13 /


Mass: 13365.560 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 / Ribosome


Mass: 7027.529 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: P0DOY6
#15: Protein 30S ribosomal protein S15 /


Mass: 10447.213 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: 9995.546 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: 11722.904 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: P0DOY7
#18: Protein 30S ribosomal protein S18 /


Mass: 8497.198 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: 9260.796 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: 10921.086 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 / Ribosome / S31


Mass: 3089.655 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, 510 molecules

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


Mass: 24.305 Da / Num. of mol.: 253 / Source method: obtained synthetically / Formula: Mg
#25: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: K
#26: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 233 / Source method: obtained synthetically / 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: 4.47 Å3/Da / Density % sol: 72.48 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5 / Details: 17% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→29.981 Å / Num. obs: 298139 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 79.82 % / Biso Wilson estimate: 144.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.83 / Rrim(I) all: 0.835 / Χ2: 0.938 / Net I/σ(I): 7.29 / Num. measured all: 23797436 / Scaling rejects: 14460
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured obsNum. possibleNum. unique obs% possible allMean I/σ(I) obsCC1/2Rmerge(I) obsRrim(I) all
2.9-2.9835.337553133224251565369.8
2.98-3.0652.8511137350218102152098.7
3.06-3.1579.1941683892212972126399.8
3.15-3.2587.3161796178205912057199.90.1
3.25-3.3588.221766510200372002499.90.290.16
3.35-3.4786.4861677312194051939499.90.470.243
3.47-3.681.0651518032187411872699.90.630.353
3.6-3.7589.6251613152180091799999.91.260.5616.136.165
3.75-3.9189.4531547001173041729499.92.010.7283.7623.783
3.91-4.188.182145976116560165541002.920.832.7452.76
4.1-4.3385.513134965715786157831004.270.9021.9221.933
4.33-4.5982.317122924614939149331006.020.9431.3581.367
4.59-4.9188.567124481614056140551009.240.9760.9220.927
4.91-5.386.7531139929131461314010012.710.9880.6660.67
5.3-5.8181.982993785121241212210016.660.9920.4940.497
5.81-6.4985.006933197109781097810021.350.9960.3650.368
6.49-7.4984.168203969748974810031.030.9980.2270.228
7.49-9.1873.626097258299828299.838.820.9990.1530.154
9.18-12.9874.4614857866524652410053.030.9990.0970.098
12.98-29.98166.7162385783769357694.958.0810.0680.069

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.3→29.981 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1392 0.67 %
Rwork0.1914 204833 -
obs0.1917 206225 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 453.76 Å2 / Biso mean: 162.4492 Å2 / Biso min: 74.99 Å2
Refinement stepCycle: final / Resolution: 3.3→29.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18910 33167 530 0 52607
Biso mean--146.5 --
Num. residues----3925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256548
X-RAY DIFFRACTIONf_angle_d0.50383912
X-RAY DIFFRACTIONf_chiral_restr0.0310425
X-RAY DIFFRACTIONf_plane_restr0.0034914
X-RAY DIFFRACTIONf_dihedral_angle_d14.26830415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.41780.36741330.3589188751900892
3.4178-3.55440.35321380.354201252026398
3.5544-3.71590.33951380.3123203942053299
3.7159-3.91140.27061390.25922055320692100
3.9114-4.15590.271390.22152057120710100
4.1559-4.47580.2641400.19222060920749100
4.4758-4.92450.1821390.16432068520824100
4.9245-5.63290.18231400.15072073920879100
5.6329-7.08140.20461410.16812088521026100
7.0814-29.98250.20471450.17032139721542100
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)
10.47030.1551-0.20050.5548-0.08850.40380.0006-0.0042-0.00380.22770.09460.12560.10340.0591-0.09341.06560.13690.05450.973-0.05491.3304143.349783.1103-12.7549
21.0367-0.27630.05060.493-0.05510.38650.0332-0.63920.40860.31140.0078-0.0875-0.21790.0707-0.0431.1913-0.25570.10981.7498-0.56741.587221.5773128.85329.3213
32.17620.962-0.9710.4362-0.57060.341-0.2325-0.0755-0.5781-0.14120.2283-0.47240.21430.13410.00591.40290.1493-0.03381.433-0.09821.7471162.781868.9453-26.0467
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886.97695.5528-4.50344.7142-3.81133.1202-1.04316.55150.8732-3.12480.50510.003-1.0062-0.09920.48951.66380.13740.06482.54630.21331.2458140.7575110.8079-74.1851
893.6545-5.5208-2.27918.4213.16092.1597-0.20470.2318-0.1626-0.80850.920.5285-0.31490.3871-0.75141.26050.0998-0.06671.41540.27761.0351144.2307104.1954-66.8188
903.0468-0.5919-4.76338.40530.10017.55030.811-2.37140.14540.8029-0.009-0.32240.18431.2177-0.75780.9213-0.0261-0.19731.2098-0.09950.9712142.9328101.6519-56.6126
915.82430.2024-4.98024.70823.4097.4763-0.12450.67-4.277-0.5052-0.7181.45772.3458-2.7350.73071.2584-0.2119-0.55961.2947-0.07642.1722130.556497.6069-64.237
929.36460.41684.56333.0795-1.78033.5535-0.0155-0.67670.36481.37630.08940.2721-0.32840.313-0.13431.67590.12320.38451.1371-0.08061.4281117.676576.410215.0401
936.6916-2.6858-0.80554.25234.92329.77490.242-0.01741.7031-0.09660.0867-0.317-0.20110.2105-0.29741.1092-00.26330.7514-0.11481.7525115.111676.935410.5464
949.26488.03059.09427.14827.58999.4919-0.2938-0.78092.1787-0.5385-0.33030.4061-1.6387-0.05160.63421.87890.07380.84451.1433-0.21882.0888109.913986.119320.6809
953.37453.85673.54134.40914.04873.712-0.0530.36031.9761-2.62460.03640.6818-2.5899-1.03230.01371.61850.33830.39651.20430.59272.3247100.829279.1315.7795
964.6477-1.81642.45253.19830.96993.3645-0.0791-1.7366-2.40761.9521-0.77741.57640.8337-0.53430.7571.9527-0.1530.70751.08720.16781.8186101.342774.610116.5914
975.25163.75110.26116.54050.36162.48120.02570.34410.4419-0.68840.4326-0.0971-0.0089-0.3873-0.45730.9367-0.044-0.06490.99130.39031.4404119.391480.6474-38.3479
987.11174.0855.51456.84684.06895.09930.2748-0.2352-0.5687-0.1090.09920.31380.11980.0015-0.31310.7909-0.06820.12371.03280.19551.2064121.410184.4996-35.5341
997.9754-6.44236.36585.1966-5.14355.05210.62662.8498-0.1091-0.9736-0.5027-0.32980.21931.0953-0.12751.5629-0.12620.05112.074-0.07641.5208137.370685.3916-44.6223
1001.9999-6.1894-5.55036.9951.81966.62620.511-1.36446.65712.22270.0897-1.0233-4.71540.5364-0.38033.5557-0.19020.53470.8929-0.14542.3885180.0515139.9381-63.8738
1011.6226-2.9384-3.50328.12797.67889.7953-0.42550.0144-0.9111-2.00920.42350.1053-0.5770.1669-0.06313.16780.20671.31221.41610.25083.082174.3899141.0504-71.4328
1022.7455-1.3725-4.69386.8957-0.77799.6-0.47560.86-0.7685-1.3174-1.2108-2.1020.45660.61781.57581.20260.25120.34411.9220.2851.9021171.7903129.0744-76.7873
1034.38954.20380.76634.40281.7682.9839-0.0872.28622.4781-3.51970.011-0.7119-4.1190.66750.03471.81830.35120.58031.45350.69321.6180.6464133.0066-74.5068
1044.7657-4.3833-3.864.79562.91443.66311.0972-2.75181.76051.60810.3609-2.8346-1.83563.0162-1.42021.1379-0.0057-0.14671.8221-0.46461.1087185.9143128.5258-66.0995
1059.2884-4.7879-5.53379.96394.60849.9131.4281-0.74341.43860.54240.4359-0.1225-0.6565-0.6547-1.72351.12-0.08460.28971.15330.160.9544175.2082126.9938-67.0171
1064.88234.97376.44287.22725.07219.5552-0.01430.6643-0.0230.32690.1015-0.9973-0.42120.5373-0.10511.25180.1030.06181.47650.09861.6272192.4404126.0021-70.8498
1079.30043.8998-7.5287.7593-0.0431.9995-1.58123.7299-0.4681-2.65391.40010.98662.891-2.93330.10041.479-0.0806-0.49862.5644-0.64441.8203251.0039112.385727.5039
1089.5935-5.92572.58094.3718-2.267.4987-2.2308-3.31540.94194.35070.6612-0.2511-1.9349-0.9791.43682.02410.21-0.46483.7644-0.69331.3385250.200499.060642.0689
1093.0140.55062.35923.8408-4.79929.2456-2.2490.40241.94972.75040.5178-3.6642-0.66341.03081.75491.5687-0.2701-0.33492.5862-0.2122.0116245.44192.338237.0913
1102.90843.26464.36045.1874.51966.624-0.0846-2.25630.21070.9665-0.23940.3063-0.3505-2.44720.36641.15760.1191-0.3064.0504-0.02871.0665245.9697104.224429.3495
1112.8519-2.6155-1.66119.6036-3.53554.5375-0.1972-1.4206-0.30950.65510.2145-1.7757-0.6216-0.034-0.02891.381-0.2223-0.14572.1235-0.09411.3068248.850795.658128.8519
1129.2923-2.63186.47135.6327-1.29284.5512-1.59970.66160.1118-0.2660.5821-0.9329-1.68881.83121.02011.771-0.1464-0.07252.0448-0.01491.5854240.167596.531917.8934
1134.0994-1.88435.96373.4755-1.78459.90970.4627-0.26-0.26720.08030.10980.4620.6052-0.2423-0.62251.1663-0.08320.35790.77920.15631.4436107.542841.7601-20.1958
1146.95070.77284.91340.09160.54063.48021.08640.76420.42390.0534-0.26840.535-0.2099-0.1053-0.78381.16050.07560.06061.91770.04391.371105.239951.3469-15.0821
1158.79416.88337.38815.53616.06567.1942-0.68971.42530.812-0.1624-0.07530.6069-2.14353.15240.78470.985-0.22250.10211.42510.64312.087102.698852.2778-31.6133
1165.1594-4.7437-3.45354.48392.81083.6762-0.9968-0.7176-1.0118-0.9097-1.66443.41871.3336-4.60392.32961.1464-0.32120.0311.8341-0.2312.045692.213447.9931-39.319
1176.3763-5.772-6.05515.2295.48235.7498-0.72-1.6372-0.1193.41740.97290.9852-0.68650.006-0.28621.7266-0.11570.37471.819-1.02092.3563250.5257123.91052.5366
1184.40564.96925.47345.61546.18146.8064-0.1144-0.64121.6879-0.41380.0588-0.3078-1.03620.89250.0111.35-0.1186-0.12861.1113-0.41431.8403246.9024129.10433.8802
1198.6878-4.9491-3.25923.09921.91631.8269-0.6235-3.34331.87384.14660.7283-2.1311-1.60071.3256-0.10862.313-0.5405-0.24332.6175-0.6341.5125253.143132.46649.9877
1204.4145-5.3708-3.98196.60744.12289.7193-0.8324-0.35921.62780.48772.6462-2.6028-0.1741.474-1.76431.1366-0.0081-0.26352.3033-0.46872.8475191.5366103.0783-1.1308
1218.7213-7.6897-0.81039.84064.04237.35330.6776-0.93690.823-0.00770.1603-1.44411.44570.7651-0.89232.0687-0.2490.03983.0008-0.22932.1402205.913392.19045.2207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)A5 - 920
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)A921 - 1400
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1532)A1401 - 1532
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)A1533 - 1541
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)B7 - 25
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)B26 - 64
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)B65 - 86
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)B87 - 122
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)B123 - 148
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)B149 - 226
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)B227 - 240
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)C2 - 112
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)C113 - 207
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)D2 - 34
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)D35 - 67
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)D68 - 148
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)D149 - 181
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)D182 - 209
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)E5 - 14
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)E15 - 27
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)E28 - 50
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)E51 - 63
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)E64 - 79
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)E80 - 86
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)E87 - 103
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)E104 - 140
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)E141 - 154
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)F1 - 32
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)F33 - 92
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)F93 - 101
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)G2 - 11
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)G12 - 20
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)G21 - 52
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)G53 - 57
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)G58 - 79
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)G80 - 92
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)G93 - 109
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)G110 - 129
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)G130 - 144
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)G145 - 156
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)H1 - 18
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)H19 - 29
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)H30 - 41
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)H42 - 53
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)H54 - 62
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)H63 - 72
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)H73 - 85
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)H86 - 95
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)H96 - 100
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)H101 - 106
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)H107 - 116
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)H117 - 127
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)H128 - 138
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)I2 - 25
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)I26 - 32
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)I33 - 53
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)I54 - 88
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)I89 - 97
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)I98 - 117
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)I118 - 128
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)J3 - 29
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)J30 - 42
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)J43 - 47
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)J48 - 70
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)J71 - 78
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)J79 - 85
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)J86 - 93
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)J94 - 100
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)K11 - 34
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)K35 - 57
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)K58 - 75
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)K76 - 100
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)K101 - 110
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)K111 - 126
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)L5 - 32
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)L33 - 128
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)M2 - 14
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)M15 - 21
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)M22 - 61
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)M62 - 83
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)M84 - 93
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)M94 - 119
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)N2 - 11
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)N12 - 16
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)N17 - 24
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)N25 - 29
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)N30 - 61
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)O2 - 15
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)O16 - 49
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)O50 - 73
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)O74 - 88
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)P1 - 19
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)P20 - 43
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)P44 - 52
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)P53 - 62
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)P63 - 83
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)Q2 - 17
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)Q18 - 82
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)Q83 - 100
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)R19 - 23
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)R24 - 28
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)R29 - 36
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)R37 - 43
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)R44 - 52
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)R53 - 76
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)R77 - 88
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)S2 - 12
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)S13 - 25
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)S26 - 35
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)S36 - 40
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)S41 - 70
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)S71 - 81
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)T8 - 66
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)T67 - 75
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)T76 - 91
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)T92 - 106
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)U2 - 8
118X-RAY DIFFRACTION118chain 'U' and (resseq 9:15)U9 - 15
119X-RAY DIFFRACTION119chain 'U' and (resseq 16:25)U16 - 25
120X-RAY DIFFRACTION120chain 'a' and (resseq 1:6)a1 - 6
121X-RAY DIFFRACTION121chain 'b' and (resseq 28:42)b28 - 42

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