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- PDB-5hl7: The crystal structure of the large ribosomal subunit of Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 5hl7
TitleThe crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with lefamulin
Components
  • (50S ribosomal protein ...) x 26
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / lefamulin / RNA / antibiotic
Function / homology
Function and homology information


large ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, C-terminal domain / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L6 / Ribosomal Protein L25; Chain P / 50s Ribosomal Protein L5; Chain: A, ...Ribosomal protein L25, C-terminal domain / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L6 / Ribosomal Protein L25; Chain P / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Aldehyde Oxidoreductase; domain 3 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / RRM (RNA recognition motif) domain / Nucleic acid-binding proteins / : / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Beta Complex / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L32p / Ribosomal protein L24 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type
Similarity search - Domain/homology
Lefamulin / ETHANOL / : / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 ...Lefamulin / ETHANOL / : / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsEyal, Z. / Matzov, D. / Krupkin, M. / Rozenberg, H. / Zimmerman, E. / Bashan, A. / Yonath, A.
CitationJournal: Sci Rep / Year: 2016
Title: A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism.
Authors: Eyal, Z. / Matzov, D. / Krupkin, M. / Paukner, S. / Riedl, R. / Rozenberg, H. / Zimmerman, E. / Bashan, A. / Yonath, A.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L2
X: 23S ribosomal RNA
Y: 5S ribosomal RNA
B: 50S ribosomal protein L3
C: 50S ribosomal protein L4
D: 50S ribosomal protein L5
E: 50S ribosomal protein L6
G: 50S ribosomal protein L13
H: 50S ribosomal protein L14
I: 50S ribosomal protein L15
J: 50S ribosomal protein L16
K: 50S ribosomal protein L17
L: 50S ribosomal protein L18
M: 50S ribosomal protein L19
N: 50S ribosomal protein L20
O: 50S ribosomal protein L21
P: 50S ribosomal protein L22
Q: 50S ribosomal protein L23
R: 50S ribosomal protein L24
S: 50S ribosomal protein L25
T: 50S ribosomal protein L27
U: 50S ribosomal protein L28
V: 50S ribosomal protein L29
W: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,365,458566
Polymers1,341,22628
Non-polymers24,232538
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area131140 Å2
ΔGint-1270 kcal/mol
Surface area467320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)282.112, 282.112, 875.343
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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50S ribosomal protein ... , 26 types, 26 molecules ABCDEGHIJKLMNOPQRSTUVWZ234

#1: Protein 50S ribosomal protein L2


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P60430
#4: Protein 50S ribosomal protein L3


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW06
#5: Protein 50S ribosomal protein L4


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW07
#6: Protein 50S ribosomal protein L5


Mass: 20296.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW18
#7: Protein 50S ribosomal protein L6


Mass: 19890.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW21
#8: Protein 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW38
#9: Protein 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW16
#10: Protein 50S ribosomal protein L15


Mass: 15021.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P0A0F8
#11: Protein 50S ribosomal protein L16


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW13
#12: Protein 50S ribosomal protein L17


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW33
#13: Protein 50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW22
#14: Protein 50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZ42
#15: Protein 50S ribosomal protein L20


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXQ1
#16: Protein 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXS8
#17: Protein 50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW11
#18: Protein 50S ribosomal protein L23


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW08
#19: Protein 50S ribosomal protein L24


Mass: 11561.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW17
#20: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2G0S0
#21: Protein 50S ribosomal protein L27


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXT0
#22: Protein 50S ribosomal protein L28


Mass: 6995.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZ60
#23: Protein 50S ribosomal protein L29


Mass: 8105.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW14
#24: Protein 50S ribosomal protein L30


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P0A0G2
#25: Protein 50S ribosomal protein L32


Mass: 6657.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZF1
#26: Protein/peptide 50S ribosomal protein L34


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FUQ0
#27: Protein 50S ribosomal protein L35


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXQ0
#28: Protein/peptide 50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW29

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RNA chain , 2 types, 2 molecules XY

#2: RNA chain 23S ribosomal RNA


Mass: 946687.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 87201381
#3: RNA chain 5S ribosomal RNA


Mass: 36692.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 87201381

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Non-polymers , 7 types, 538 molecules

#29: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 274 / Source method: obtained synthetically / Formula: Mn
#30: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 240 / Source method: obtained synthetically / Formula: Mg
#31: Chemical ChemComp-62B / Lefamulin


Mass: 507.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H45NO5S / Comment: medication, antibiotic*YM
#32: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#33: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H19N3
#34: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#35: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

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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: 3.76 Å3/Da / Density % sol: 67.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1:2 MPD:EtOH 10mM Hepes pH=7.6 10mM Mg2Cl 60mM NH4Cl 15mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.971 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 3.55→50 Å / Num. obs: 236087 / % possible obs: 95.7 % / Redundancy: 11 % / Biso Wilson estimate: 105.61 Å2 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.055 / Rrim(I) all: 0.213 / Χ2: 1.075 / Net I/av σ(I): 9 / Net I/σ(I): 5 / Num. measured all: 2606786
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.55-3.619.20.994115040.6260.31.03594.6
3.61-3.688.90.867115060.7050.2661.07394.80.913
3.68-3.758.50.727115080.8120.231.07794.60.767
3.75-3.8290.658114620.8090.21.07694.20.692
3.82-3.919.60.548115240.8520.1591.04894.80.574
3.91-49.60.5114950.8790.1451.0894.40.524
4-4.19.50.452115580.8950.1321.07194.60.474
4.1-4.219.40.403115670.9130.1191.07894.60.423
4.21-4.339.30.35115250.9350.1041.06394.60.368
4.33-4.479.10.315115660.940.0951.08594.30.331
4.47-4.638.40.277115750.9510.0881.09294.60.292
4.63-4.829.10.25115700.9550.0761.07594.50.263
4.82-5.0410.10.252116900.960.0711.04594.80.264
5.04-5.314.90.365120680.9530.0851.0998.30.376
5.3-5.6314.60.302121560.9690.0711.08398.30.312
5.63-6.0713.80.267120980.9730.0661.08797.90.277
6.07-6.6814.40.232121990.9760.0561.059980.24
6.68-7.6414.80.185122670.9830.0441.07697.90.191
7.64-9.6113.50.151123630.9880.0381.09797.70.156
9.61-5013.70.116128860.990.0291.07796.90.121

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WCE

4wce


Resolution: 3.55→49.93 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 11845 5.02 %
Rwork0.1869 223966 -
obs0.1888 235811 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 286.33 Å2 / Biso mean: 110.8392 Å2 / Biso min: 45.07 Å2
Refinement stepCycle: final / Resolution: 3.55→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20308 60413 741 0 81462
Biso mean--100.01 --
Num. residues----5808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188398
X-RAY DIFFRACTIONf_angle_d1.61133592
X-RAY DIFFRACTIONf_chiral_restr0.07117454
X-RAY DIFFRACTIONf_plane_restr0.0076515
X-RAY DIFFRACTIONf_dihedral_angle_d17.11940843
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5464-3.58670.31633670.27246611697886
3.5867-3.62890.30893890.26227308769795
3.6289-3.67310.29423920.25397289768195
3.6731-3.71960.28234040.23767308771295
3.7196-3.76850.28874030.23487270767394
3.7685-3.82010.25993680.23257305767394
3.8201-3.87470.25133420.21797329767195
3.8747-3.93250.25513890.20767329771895
3.9325-3.99390.25633960.21217301769795
3.9939-4.05940.23334130.20897291770495
4.0594-4.12940.27684080.20147321772995
4.1294-4.20440.22743570.18887380773795
4.2044-4.28520.22984030.18447314771794
4.2852-4.37270.21983580.18237292765094
4.3727-4.46770.21253930.18587370776395
4.4677-4.57150.23433920.17567313770594
4.5715-4.68580.22454130.17557384779795
4.6858-4.81240.21193810.17077346772794
4.8124-4.95390.20233770.16917348772594
4.9539-5.11360.2113910.16827572796397
5.1136-5.29620.21654010.15957702810398
5.2962-5.5080.19924090.15827711812098
5.508-5.75830.19343760.15627730810698
5.7583-6.06140.21584330.1547655808898
6.0614-6.44040.20584010.15967740814198
6.4404-6.93650.20043740.15577776815098
6.9365-7.63230.19724400.15587787822798
7.6323-8.73160.22214070.16337823823098
8.7316-10.98160.19074230.16577897832097
10.9816-49.93520.24254450.22958164860996
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)
10.5545-0.0022-0.12220.4021-0.12210.3998-0.0810.58630.4127-0.18430.0117-0.0639-0.2268-0.0880.08590.8720.0198-0.01571.36590.55550.894221.9446-64.3893-60.1431
20.7301-0.1312-0.10190.33970.05540.2998-0.09030.0530.35290.10320.0317-0.0525-0.2442-0.04790.08490.8230.1734-0.07310.71460.22290.760619.9147-64.6349-8.1739
30.8142-0.0928-0.14150.39450.06330.3867-0.09890.16880.2610.0540.0270.0832-0.1892-0.20040.07770.73580.18310.0580.82830.21270.5778-4.1208-76.8659-16.9069
41.04560.2608-0.2630.12950.03960.6452-0.1895-0.30250.81130.03440.0766-0.0023-0.29610.10220.07291.1810.279-0.15720.7273-0.01921.39615.7093-36.74310.6827
50.74420.0611-0.08560.3812-0.05650.4462-0.1368-0.24590.16550.23860.0297-0.0726-0.1368-0.04060.09880.77010.254-0.00760.74850.08330.569118.2689-82.69022.7132
60.92870.01120.20170.4614-0.07361.0126-0.3491-0.21820.46470.09220.1644-0.2858-0.33410.27450.20290.92750.0476-0.33241.0157-0.00411.2124102.9485-82.268815.0324
70.15340.1381-0.11780.1643-0.15650.1384-0.0255-0.03680.25610.42410.1094-0.1557-0.2818-0.1308-0.1131.47780.2895-0.070.60910.15681.7747-5.9043-17.9934-11.8178
80.86210.1763-0.25980.5932-0.11890.2012-0.00790.1609-0.08980.33320.0950.20280.0235-0.1694-0.06850.97960.1720.35540.9920.12530.6562-18.9982-121.954114.1547
90.30180.1117-0.5340.2617-0.1650.9102-0.20930.50670.0211-0.14280.0807-0.062-0.0602-0.12490.04270.7082-0.18780.09561.56280.40070.681739.9986-85.4598-72.983
104.5105-1.43870.0871.4572-1.4482.01470.3086-1.40470.41281.2270.3044-0.9222-0.06060.6413-0.5771.59280.054-0.52821.456-0.37851.4917104.8619-49.287236.4469
110.7688-1.07970.07721.5706-0.01940.13240.09350.2111-0.62770.45010.05071.08480.362-0.0605-0.15471.06890.41870.31461.16920.39342.265924.0513-135.301151.1397
121.26330.6226-0.06080.4154-0.10010.6112-0.113-0.3727-0.52610.5149-0.00290.01690.0955-0.27550.09320.95380.31830.24490.73840.21480.801122.2527-136.7042.1431
131.42050.9302-0.18260.78130.00571.27640.1622-0.5350.21950.6626-0.16250.2739-0.0241-0.084-0.00511.53470.420.22021.5584-0.07090.5925-20.1746-85.910541.2431
141.6490.7155-0.18522.37820.22712.864-0.2632-1.26250.0590.5046-0.2412-0.26960.44030.21390.48820.79380.2201-0.07151.55490.03660.661157.5794-89.8331.1462
152.53-0.2826-0.46971.82090.73460.3488-0.01080.23120.03440.2065-0.21410.5505-0.1054-0.90250.21410.47130.19780.23361.05470.1140.7538-48.3806-101.8331-13.9565
162.77670.5338-1.8361.45870.30162.8241-0.38150.43010.59770.1937-0.0737-0.7048-0.30980.46410.43450.6373-0.1412-0.34520.87090.3241.5847117.773-66.7711-1.9682
172.4932-0.0744-1.37263.51960.57361.6326-0.0936-0.49340.0510.48830.07730.2774-0.0527-0.11170.01260.84040.34440.36311.41020.06430.7744-42.7911-98.695632.4881
181.338-0.68630.15051.5192-0.29810.633-0.28750.211-0.43270.20850.154-0.00990.0889-0.07970.12130.62230.1630.34770.75760.07560.677235.469-127.4057-23.258
191.4989-0.2586-0.13612.0680.12911.7337-0.01040.5066-0.4366-0.235-0.22540.02060.58450.36270.21520.54470.11210.26370.6712-0.01810.7143.6296-134.8646-35.1406
201.94161.14210.70623.12130.18351.7055-0.37690.191-0.3292-0.31780.35110.08660.4256-0.38040.05630.6676-0.11330.1961.30130.10850.5859-14.8657-111.0819-39.6728
212.6864-0.58680.88032.1799-1.14592.8322-0.08710.12110.0624-0.09760.01210.0023-0.1937-0.65310.02451.01470.2901-0.04931.52030.67971.2128-34.7505-60.7925-62.2885
223.47680.90670.59232.1586-0.68353.2237-0.18980.96930.0682-0.13110.2686-0.35540.168-0.5667-0.16740.7087-0.17390.10851.8408-0.02850.7235-4.2614-95.93-90.4977
233.4864-0.3894-0.40913.49251.07512.2075-0.1289-1.00550.30750.50320.4159-0.17180.28550.1498-0.26620.80390.2635-0.14581.23820.12530.804783.1046-107.854334.9331
245.7985-0.9379-1.12743.09350.69772.6930.036-0.83010.27960.0656-0.1631-0.93760.21130.45690.16240.6418-0.0019-0.22440.77580.23781.062884.6876-77.068-8.1695
252.218-0.4955-1.08962.90890.88290.68130.29680.1253-0.1255-0.3794-0.15080.1308-0.1076-0.2811-0.13842.16960.2568-0.10361.5221.00662.443825.0966-24.785-41.3529
262.12860.5126-0.01790.6-0.03241.7913-0.13920.49480.5239-0.4582-0.0441-0.13880.4803-0.14190.18921.94510.6144-0.2192.30730.48320.9817-25.2202-59.2235-83.9137
277.73090.7853-1.22743.42151.51755.5481-0.20290.1322-0.2456-0.11260.0783-0.83030.49840.15080.11820.59560.03590.05210.55930.09840.768668.7796-113.7764-15.3595
281.6244-0.5088-0.42460.9663-0.3030.9108-0.34270.4397-0.71940.14030.21460.24310.3932-0.42940.11130.6157-0.05150.35240.96660.13130.6011-14.7962-113.6837-24.5189
290.60580.02690.13840.4063-0.20691.0047-0.01180.19470.3495-0.07150.00080.1037-0.2611-0.2389-0.04920.75740.092-0.11791.37120.59990.9977-3.4025-54.7272-43.1261
301.3054-0.3603-0.43231.2051-0.32530.332-0.268-0.05380.1677-0.0960.4258-0.0082-0.0149-0.1493-0.14580.5496-0.0229-0.09870.81390.34690.869163.7041-61.6483-33.2823
313.30860.42491.01491.22110.15568.87570.31410.1156-0.1840.12560.25440.23330.3715-0.5019-0.51682.6871-0.1679-0.162.06210.38651.352236.1488-112.468943.6527
320.73760.4776-0.16130.3791-0.10410.0558-0.14140.4681-0.0545-0.11250.0324-0.3302-0.23640.30110.0810.7795-0.08350.10041.30870.45610.903963.5328-70.2218-53.6786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'X' and (resid 2 through 722 )X0
2X-RAY DIFFRACTION2chain 'X' and (resid 723 through 948 )X0
3X-RAY DIFFRACTION3chain 'X' and (resid 949 through 1790 )X0
4X-RAY DIFFRACTION4chain 'X' and (resid 1791 through 2021 )X0
5X-RAY DIFFRACTION5chain 'X' and (resid 2022 through 2921 )X0
6X-RAY DIFFRACTION6chain 'Y' and (resid 1 through 114 )Y0
7X-RAY DIFFRACTION7chain 'A' and (resid 3 through 271 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 216 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 201 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 5 through 179 )D0
11X-RAY DIFFRACTION11chain 'E' and (resid 18 through 174 )E0
12X-RAY DIFFRACTION12chain 'G' and (resid 1 through 142)G0
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 122 )H0
14X-RAY DIFFRACTION14chain 'J' and (resid 1 through 141 )J0
15X-RAY DIFFRACTION15chain 'K' and (resid 4 through 122 )K0
16X-RAY DIFFRACTION16chain 'L' and (resid 5 through 111 )L0
17X-RAY DIFFRACTION17chain 'M' and (resid 1 through 110 )M0
18X-RAY DIFFRACTION18chain 'N' and (resid 2 through 117 )N0
19X-RAY DIFFRACTION19chain 'O' and (resid 1 through 101 )O0
20X-RAY DIFFRACTION20chain 'P' and (resid 1 through 112 )P0
21X-RAY DIFFRACTION21chain 'Q' and (resid 2 through 91 )Q0
22X-RAY DIFFRACTION22chain 'R' and (resid 3 through 102 )R0
23X-RAY DIFFRACTION23chain 'S' and (resid 3 through 169 )S0
24X-RAY DIFFRACTION24chain 'T' and (resid 19 through 94 )T0
25X-RAY DIFFRACTION25chain 'U' and (resid 13 through 54 )U0
26X-RAY DIFFRACTION26chain 'V' and (resid 2 through 66 )V0
27X-RAY DIFFRACTION27chain 'W' and (resid 2 through 58 )W0
28X-RAY DIFFRACTION28chain 'Z' and (resid 2 through 44 )Z0
29X-RAY DIFFRACTION29chain '2' and (resid 2 through 44 )20
30X-RAY DIFFRACTION30chain '3' and (resid 2 through 61 )30
31X-RAY DIFFRACTION31chain '4' and (resid 1 through 36 )40
32X-RAY DIFFRACTION32chain 'I' and (resid 1 through 131 )I0

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