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- PDB-6caq: Crystal Structure of 30S ribosomal subunit from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 6caq
TitleCrystal Structure of 30S ribosomal subunit from Thermus thermophilus
Components
  • (30S ribosomal protein ...) x 20
  • 16S Ribosomal RNA rRNA
  • RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
  • RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
KeywordsRIBOSOME / translation / miscoding / antibiotic / N1MS
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 / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
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 S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B ...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 S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Helix hairpin bin / Ribosomal Protein S7 / Ribosomal protein S7/S5 / 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 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 S14/S29 / 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 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. / Ribosomal protein S2 signature 1. / Nucleotidyltransferase; domain 5 / 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 S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / : / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Helix Hairpins / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site
Similarity search - Domain/homology
Chem-EUS / : / 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 ...Chem-EUS / : / 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)
Thermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsDeMirci, H.
CitationJournal: To Be Published
Title: Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
Authors: DeMirci, H.
History
DepositionJan 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Y: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
W: RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)782,774426
Polymers772,39623
Non-polymers10,378403
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)400.970, 400.970, 175.050
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 AYW

#1: RNA chain 16S Ribosomal RNA rRNA


Mass: 494168.781 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(*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria)
#23: RNA chain RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')


Mass: 4815.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria)

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

#2: Protein 30S ribosomal protein S2


Mass: 26987.271 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: 22862.430 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: 16331.079 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: 11299.176 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: 12319.034 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: 13850.402 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


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: 10390.160 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: 9924.469 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: 11721.919 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: 8155.812 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: 9203.743 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 / S31


Mass: 2960.475 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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Sugars , 1 types, 1 molecules

#25: Sugar ChemComp-EUS / N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]methanesulfonamide


Type: saccharide / Mass: 525.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H39N5O9S

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Non-polymers , 3 types, 658 molecules

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


Mass: 24.305 Da / Num. of mol.: 400 / Source method: obtained synthetically / Formula: Mg
#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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 73.2 %
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: 3.13→39.908 Å / Num. obs: 242707 / % possible obs: 97.4 % / Redundancy: 77.741 % / Biso Wilson estimate: 68.08 Å2 / CC1/2: 0.865 / Rmerge(I) obs: 2.439 / Rrim(I) all: 2.455 / Χ2: 0.839 / Net I/σ(I): 8.45 / Num. measured all: 18868280 / Scaling rejects: 2804
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
3.13-3.2141.74914.2120.33531133182571272214.36969.7
3.21-3.2967.41912.2250.571165195177561728312.31597.3
3.29-3.3980.14510.1610.791387550173471731310.22499.80.22
3.39-3.4981.068.660.98136415616834168298.7141000.305
3.49-3.6181.2077.081.23132530016326163207.1241000.404
3.61-3.7480.1445.4451.6126700115812158095.4791000.555
3.74-3.8875.3864.2641.99114834815277152334.29399.70.633
3.88-4.0484.3083.0262.93123848414691146903.0441000.798
4.04-4.2184.5632.263.94119335014112141122.2731000.866
4.21-4.4283.1541.755.15112499213530135291.761000.916
4.42-4.6680.611.3546.71103792812877128761.3621000.948
4.66-4.9478.3051.0898.3294827112178121101.09699.40.949
4.94-5.2884.2620.8511.1296943811506115050.8551000.982
5.28-5.7183.0790.66913.6988811210692106900.6731000.988
5.71-6.2579.0360.55315.69784196992599220.5571000.99
6.25-6.9982.4040.40420.57730427895388640.407990.992
6.99-8.0782.410.25530.3656560796779670.2561000.998
8.07-9.8875.2980.18237.45505477678267130.183990.998
9.88-13.9877.0990.1256.21410707532753270.1211000.999
13.98-39.90866.2480.09359.44191655310028930.09493.31

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementResolution: 3.4→39.908 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 1595 0.82 %
Rwork0.1897 191873 -
obs0.1899 193468 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 544.82 Å2 / Biso mean: 78.9858 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3.4→39.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19088 32943 693 0 52724
Biso mean--73.91 --
Num. residues----3910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456716
X-RAY DIFFRACTIONf_angle_d0.83984184
X-RAY DIFFRACTIONf_chiral_restr0.04410528
X-RAY DIFFRACTIONf_plane_restr0.0054910
X-RAY DIFFRACTIONf_dihedral_angle_d16.97330817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.50970.31691430.31221732317466100
3.5097-3.6350.30951440.28891730717451100
3.635-3.78050.31641440.26111734617490100
3.7805-3.95240.2421430.2346172311737499
3.9524-4.16060.26771460.20131740317549100
4.1606-4.42090.20971440.17371738917533100
4.4209-4.76180.17361440.16041741517559100
4.7618-5.240.1751450.14291743817583100
5.24-5.9960.20271460.13611758117727100
5.996-7.5460.18711470.1471175911773899
7.546-39.91070.16721490.1652178491799898
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)
10.44740.1853-0.22530.4856-0.09310.36450.05840.02910.01530.21480.07690.14540.07170.0137-0.12570.4050.09990.08230.2998-0.02790.634143.749483.4993-12.7811
21.5739-0.16950.08430.4678-0.01510.36160.0771-0.77360.51680.2843-0.0124-0.0884-0.21880.1652-0.0280.6083-0.27420.13761.075-0.5980.8409222.2662129.57229.0441
31.46460.5506-0.64990.093-0.31940.1353-0.1147-0.033-0.3710.02720.1978-0.21580.21790.0359-0.00680.44040.0876-0.00560.4956-0.10350.8357164.666270.1114-26.3658
49.4341-6.59438.03444.9598-6.40788.7714-0.5339-2.1361-0.97471.34992.60842.455-0.7602-0.1232-2.0961.1620.49190.1762.40870.32441.4038203.5025111.7696-33.7402
53.06433.64360.96534.55310.90520.5688-0.4928-0.01250.4698-0.76960.5874-1.422-0.54310.3127-0.07431.37560.13890.43230.47510.14281.4571155.253157.9186-35.0815
61.2141-0.16731.51254.22151.88323.6940.0196-0.13420.4177-0.526-0.55411.2278-0.9352-0.72630.54421.00940.1560.39670.38970.00971.6356149.3904156.1262-27.9786
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919.8129-1.70320.33853.33294.01655.60340.18650.1416-3.05780.3624-0.51630.9291.094-1.71430.28950.5848-0.1208-0.24630.92840.2251.3279130.821697.9287-64.2099
924.56240.98953.78262.11341.82124.6830.11530.0280.08520.50540.1615-0.21980.28040.1801-0.26080.8090.02750.44190.30380.02260.6407117.985776.797515.1266
931.20760.77730.38255.31380.91642.596-0.09610.04520.3265-0.06960.4011-0.1972-0.02560.0603-0.20620.5931-0.06510.35920.2175-0.01990.9628115.467177.252710.6227
942.00027.88139.39436.33817.17498.4306-0.25490.381.885-0.58010.1940.2361-2.68340.27570.03340.95920.04690.52470.51970.02741.0389110.159886.469420.592
951.13462.4569-0.33825.6563-1.47081.724-0.0164-0.01450.3375-0.1180.09430.6543-0.5784-0.1524-0.11380.59910.12970.27060.28650.32911.0086101.254879.31255.8265
963.36674.2870.44797.3482-1.76433.47720.2364-0.34750.24030.9607-0.09530.8833-0.2926-0.2368-0.18870.7890.0120.48720.28520.12741.031101.654374.992616.5637
973.22974.85131.388.33580.99111.715-0.20830.58340.2999-0.81450.644-0.7222-0.34520.3261-0.44880.2217-0.0803-0.06850.50920.14240.7083119.960780.8341-38.5514
980.79380.4824-1.20692.4797-1.17612.0794-0.23780.2164-0.0482-0.5360.39840.61450.1873-0.2299-0.18360.2891-0.0920.0080.27430.11530.7967121.956284.7382-35.7223
995.2881-5.2063.85195.1767-3.93516.06610.36930.64770.667-0.3931-0.1505-0.9015-0.49140.8257-0.22170.5155-0.23710.08060.65160.01220.8411137.991585.8775-44.9368
1009.8162-8.22373.22848.7354-2.65754.9871-0.6511-1.13024.4405-0.07470.3181-1.2666-3.0793-0.29090.3121.40950.12420.47110.6682-0.16351.6599180.1638140.1171-64.322
10126.4658.82854.45776.14538.476-3.1645-0.5655.8234-0.36610.30271.1151-4.5231-0.60542.86392.3540.21420.40980.75760.092.2267175.0085141.6864-72.1705
1027.6239-5.8592-6.15735.14265.75186.5977-0.15750.3454-0.644-0.7346-0.2763-1.50130.21850.49390.43760.72380.21240.31371.15170.42860.9439172.3953129.1958-77.3401
1032.8398-0.74353.34213.52211.24585.28410.89821.15071.9843-1.4511-0.4898-1.6056-1.4516-0.0644-0.44120.82530.3780.5110.7130.39631.2066181.2386133.2403-75.177
1046.6519-2.2011-3.95383.264-0.97396.6750.42-0.13121.4936-0.51250.1659-2.32850.12641.9474-0.56690.5290.33220.16690.8916-0.14661.0026186.3783128.5988-66.6799
1059.427-6.2181-6.75616.38465.52717.2780.3023-0.1680.44610.14020.18970.0493-0.6442-0.2322-0.42770.47160.10750.22590.470.21890.5897175.7526127.0973-67.6738
1062.382-2.01321.16422.1051-1.55551.3792-0.0148-0.32950.419-0.0455-0.0401-0.2622-0.32450.28220.10270.64370.24060.17850.6952-0.00030.9015192.963126.0191-71.41
1070.34120.3273-0.87658.5307-7.37477.4452-0.29212.9169-1.0854-2.33150.67241.06342.3709-1.8134-0.41831.1255-0.3559-0.35492.1805-0.27861.1568251.731113.021627.8726
1084.4416-3.60063.9833.3267-3.77076.0341-1.877-3.71321.43475.12051.0226-1.5515-1.54810.47290.80981.67870.018-0.3771.7686-0.19550.9943250.7535100.119642.2177
1098.52975.71015.81299.21211.77098.0851-0.2269-0.348-0.55810.6448-0.4369-0.67350.1242-1.04850.66760.8381-0.358-0.05862.3929-0.06721.2672246.133693.677636.953
1102.00016.31399.79715.98953.4298.59290.956-7.67063.98121.1728-1.24150.8342-2.2028-3.18450.27371.238-0.31550.16741.8714-0.47410.9098246.3051105.011228.8946
1119.0755-0.37718.11318.0805-1.38059.0041-0.3546-1.2879-0.3050.56190.214-0.8839-0.58090.540.10530.6802-0.1077-0.05541.7056-0.06950.5601249.375696.440328.8799
1124.4728-0.3725.14578.572-1.70966.1119-0.54091.315-0.8024-0.74670.443-1.4089-0.68721.56670.0760.5525-0.28160.09471.6451-0.21980.7384240.984397.033317.952
1131.8176-1.15812.92312.2129-2.77847.76420.38470.09960.0232-0.06940.06150.52860.5917-0.3203-0.41660.5382-0.12080.24680.24260.15120.9064108.029441.995-20.1677
1143.35831.43480.79142.0247-0.33410.50580.1826-1.22610.06392.90731.11242.8474-2.2871-1.4962-1.27140.99390.20390.1730.61730.29150.9022105.646951.9076-14.7933
1152.17433.22333.28845.30525.49516.1077-0.32330.61530.3157-0.79330.5084-0.4769-1.69151.032-0.19420.5615-0.14820.04370.49950.25631.0347103.200652.3466-31.6311
1167.7634-4.7551-1.91044.10612.61183.57620.55110.1965-1.2238-0.109-0.89982.61581.4073-2.53780.31950.7092-0.2644-0.09550.90630.15261.19192.640648.0728-39.6451
1174.5151-0.02486.22923.08270.45578.6741.2666-0.61-1.45160.4864-0.40070.02840.50110.11-0.88690.4981-0.29960.00881.0449-0.42921.2164250.9403124.40061.9375
1183.8365-3.70624.13065.2475-1.75978.285-0.32760.3469-0.7795-0.56930.363-0.7372-0.32750.4501-0.02640.6003-0.2099-0.11970.7189-0.39530.9677247.8597129.61713.7226
1191.5494-0.1410.40310.91750.09742.6969-0.1745-0.42130.55880.9916-0.0402-0.7302-0.6070.19720.1681.1213-0.3975-0.32081.1342-0.48821253.7883132.87549.8549
1207.58024.8266-5.57049.0313-5.46727.8555-0.3873-1.75162.83940.82920.73490.8966-1.3461-0.928-0.30830.99510.3661-0.5271.4272-0.57441.7201191.7456103.6921-1.091
1214.02521.6712-2.53364.8890.10071.90850.2794-1.3555-0.05131.4848-0.074-1.57961.00341.7505-0.18220.85690.2506-0.30351.9423-0.58641.2269205.922293.03026.2777
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 'Y' and (resseq 1:6)Y1 - 6
121X-RAY DIFFRACTION121chain 'W' and (resseq 28:42)W28 - 42

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