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- PDB-4wfb: The crystal structure of the large ribosomal subunit of Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 4wfb
TitleThe crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with BC-3205
Components
  • (50S ribosomal protein ...) x 26
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
KeywordsRIBOSOME / RNA / bacteria
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / rRNA binding / ribosome ...large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / 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 / Helix Hairpins - #310 / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L6 / Ribosomal Protein L25; Chain P ...Ribosomal protein L25, C-terminal domain / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Helix Hairpins - #310 / 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. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Beta Complex / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, 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 L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L28/L24 / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / 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 L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4
Similarity search - Domain/homology
BC-3205 / ETHANOL / : / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 ...BC-3205 / 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 bL25 / 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)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsEyal, Z. / Matzov, D. / Krupkin, M. / Wekselman, I. / Zimmerman, E. / Rozenberg, H. / Bashan, A. / Yonath, A.E.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.
Authors: Zohar Eyal / Donna Matzov / Miri Krupkin / Itai Wekselman / Susanne Paukner / Ella Zimmerman / Haim Rozenberg / Anat Bashan / Ada Yonath /
Abstract: The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from ...The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.
History
DepositionSep 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Jan 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 23S rRNA
Y: 5S rRNA
A: 50S ribosomal protein L2
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)1,367,046494
Polymers1,341,76128
Non-polymers25,285466
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • 28-mer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area136200 Å2
ΔGint-1338 kcal/mol
Surface area467440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)280.918, 280.918, 875.585
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Detailsbiological unit is the same as asym.

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Components

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RNA chain , 2 types, 2 molecules XY

#1: RNA chain 23S rRNA / 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
#2: RNA chain 5S rRNA / 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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50S ribosomal protein ... , 26 types, 26 molecules ABCDEGHIJKLMNOPQRSTUVWZ234

#3: Protein 50S ribosomal protein L2 /


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / References: UniProt: Q2FW18
#7: Protein 50S ribosomal protein L6 /


Mass: 19818.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / References: UniProt: Q2FW16
#10: Protein 50S ribosomal protein L15 /


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / References: UniProt: Q2FJE0, UniProt: Q2G0S0*PLUS
#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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / 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 (bacteria) / Strain: NCTC 8325 / References: UniProt: Q2FW29

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Non-polymers , 7 types, 466 molecules

#29: Chemical ChemComp-3LK / BC-3205


Mass: 578.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H54N2O5S
#30: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#31: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 111 / Source method: obtained synthetically / Formula: Mg
#32: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 311 / Source method: obtained synthetically / Formula: Mn
#33: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#34: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C7H19N3
#35: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O

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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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Hepes, KCl, MgCl2, NH4Cl, MPD, EtOH, Spermidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.43→50 Å / Num. obs: 253918 / % possible obs: 92.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 98.31 Å2 / Rmerge(I) obs: 0.152 / Χ2: 1.046 / Net I/av σ(I): 10.516 / Net I/σ(I): 6 / Num. measured all: 2109298
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.43-3.473.40.74471750.82778.9
3.47-3.514.60.71878030.85586.3
3.51-3.555.40.66780730.87288.8
3.55-3.65.90.62681660.88790.1
3.6-3.646.60.6181330.89389.8
3.64-3.697.10.55583460.91491.9
3.69-3.757.40.47283550.98292.1
3.75-3.87.70.4783920.99392.4
3.8-3.867.90.45184261.0292.6
3.86-3.9380.39984621.06892.8
3.93-3.998.30.38784371.09892.8
3.99-4.078.70.36384371.08692.9
4.07-4.148.70.33984821.09993.2
4.14-4.238.60.3185341.10293.3
4.23-4.328.60.28684971.05993.4
4.32-4.428.70.26784851.13192.7
4.42-4.538.60.24985491.0793.8
4.53-4.658.60.21685241.08793.2
4.65-4.798.60.20785591.06693.3
4.79-4.958.60.19285081.06693
4.95-5.128.60.17885411.07192.8
5.12-5.338.50.16685271.07292.7
5.33-5.578.50.15485741.06993
5.57-5.868.50.15185151.07392.3
5.86-6.238.50.14285571.0792.3
6.23-6.718.40.13986041.07792.5
6.71-7.388.20.13185591.08291.8
7.38-8.458.20.11885201.02190.5
8.45-10.6212.80.16791801.09996.2
10.62-5015.90.09899981.04399.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WCE

4wce


Resolution: 3.43→49.539 Å / FOM work R set: 0.8389 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 12763 5.03 %Random selection
Rwork0.2042 240887 --
obs0.2061 253650 91.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 286.77 Å2 / Biso mean: 80.29 Å2 / Biso min: 0.03 Å2
Refinement stepCycle: final / Resolution: 3.43→49.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19929 60464 791 0 81184
Biso mean--87.3 --
Num. residues----5771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00688187
X-RAY DIFFRACTIONf_angle_d1.099133279
X-RAY DIFFRACTIONf_chiral_restr0.05817419
X-RAY DIFFRACTIONf_plane_restr0.0066450
X-RAY DIFFRACTIONf_dihedral_angle_d16.93740749
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 (%)
3.4062-3.44490.32353420.29776189653172
3.4449-3.48540.32663780.29217414779286
3.4854-3.52790.32074340.27297649808389
3.5279-3.57250.29054270.26417741816890
3.5725-3.61950.3083930.25767789818290
3.6195-3.66910.27584070.24967943835092
3.6691-3.72150.28984140.23547969838392
3.7215-3.7770.28634580.23527943840192
3.777-3.8360.284240.23118024844893
3.836-3.89890.26493950.21268082847793
3.8989-3.96610.24753940.21528045843993
3.9661-4.03820.24584340.20378031846593
4.0382-4.11580.23914460.20748066851293
4.1158-4.19980.26124290.20318118854793
4.1998-4.29110.25234610.19628043850493
4.2911-4.39080.23213990.19228111851093
4.3908-4.50060.22834230.19028131855494
4.5006-4.62220.22594340.18318112854693
4.6222-4.75810.22994290.17588137856693
4.7581-4.91150.22094490.17548105855493
4.9115-5.08690.22614490.17718097854693
5.0869-5.29030.21794260.16918113853993
5.2903-5.53080.20944360.15718149858593
5.5308-5.8220.18814280.15628095852392
5.822-6.18610.21224110.16288160857192
6.1861-6.66270.21434200.17068215863593
6.6627-7.33130.20964570.16388109856692
7.3313-8.38770.234090.17418128853791
8.3877-10.55080.23484480.19578735918396
10.5508-49.54440.25975090.262294449953100
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)
10.5927-0.1571-0.14360.2601-0.1440.3684-0.05830.59760.4103-0.1548-0.0695-0.063-0.2304-0.0836-0.06020.58380.0074-0.04991.06810.65530.567122.2591-64.0514-60.2784
20.33690.0809-0.08510.15330.10210.2742-0.00720.14460.30880.0331-0.0324-0.064-0.3247-0.07180.06370.6110.1886-0.03760.44420.21860.57120.7434-64.3503-7.588
30.7405-0.1249-0.14120.37370.04220.3309-0.07960.15020.19190.0440.05240.0718-0.2166-0.23820.07880.45310.23540.0050.67920.22090.37-4.1586-75.967-17.1879
40.82050.2168-0.35070.09040.16530.3982-0.077-0.35860.7536-0.00470.1320.1808-0.3148-0.0055-0.0841.0260.3142-0.14620.5413-0.03491.064515.574-36.74241.4541
50.58590.0013-0.07530.272-0.03380.3388-0.131-0.190.16250.30850.0449-0.1243-0.2201-0.1070.04240.39660.24240.0450.60140.11770.367118.5054-82.36082.7643
60.22520.183-0.04950.5009-0.05360.2708-0.0623-0.1171-0.02240.20790.098-0.27350.05450.0781-0.01210.54780.0476-0.24740.77910.01870.8081103.1782-81.50615.1123
70.0071-0.0165-0.01680.14650.08860.04290.04220.03160.1624-0.0028-0.02080.0725-0.1485-0.12210.05491.00650.3981-0.10820.40550.20061.0817-5.8327-17.5801-11.5444
80.16160.0593-0.12730.19650.01180.1393-0.001-0.0014-0.05520.09760.05060.07950.0221-0.06890.16440.41020.14960.27340.73540.11040.3155-18.6056-121.668914.2574
90.31670.0842-0.32770.1558-0.09790.4523-0.10160.261-0.0274-0.0515-0.0013-0.0972-0.03610.11670.06420.4733-0.19470.12810.93580.33710.431940.3121-85.1239-72.7411
101.0586-0.38850.52960.5082-0.52150.65060.0104-0.38920.37820.30020.0872-0.3039-0.30820.2041-0.00541.3545-0.1892-0.46791.1048-0.42771.1458106.4973-50.063435.3016
110.4531-0.1222-0.13120.56860.12830.18580.0548-0.0214-0.13920.1915-0.02470.11860.0781-0.1162-0.02240.47290.1860.12430.68630.4660.840824.6998-135.32751.9098
120.6118-0.0765-0.03150.7014-0.11010.369-0.1774-0.093-0.45350.1940.1118-0.01810.0557-0.27030.06680.41580.15420.1810.56660.09230.619722.5908-136.14552.0436
130.63520.3409-0.47510.2618-0.1040.90770.0566-0.26280.13570.2463-0.0710.135-0.05510.0433-0.07020.85540.3850.22081.1558-0.07380.3822-20.0267-85.340941.1083
140.49880.10190.31610.5924-0.49911.4513-0.0907-0.32590.03630.2349-0.0999-0.1179-0.04170.01880.05360.42790.1464-0.13140.86380.06240.471457.9135-88.821231.1916
151.5569-0.2552-0.89311.04430.40050.69730.00920.17890.04020.0082-0.12770.3084-0.024-0.34940.02340.27070.1740.19850.7789-0.00410.476-47.7071-101.741-13.7558
161.5350.0159-0.96320.59780.06641.9116-0.1561-0.02440.1068-0.0595-0.0395-0.23-0.04540.07290.09190.3567-0.1587-0.08450.65420.13411.1624117.5516-65.4974-0.6512
170.9992-0.4662-0.74751.15480.47320.7623-0.0878-0.037-0.09660.0718-0.04510.09320.0438-0.0144-0.06360.50980.23640.35260.8914-0.05030.4036-42.6131-98.85233.1214
180.4711-0.14-0.20440.2545-0.02950.5019-0.07420.0107-0.0490.07330.07230.03770.17310.0380.27870.24160.09740.28110.37240.15160.320135.8843-126.8412-23.3692
190.3364-0.4384-0.02931.48070.23790.1238-0.09450.1102-0.27590.00750.0256-0.11460.34470.14990.02850.630.29760.23490.5466-0.00470.467944.2645-134.4623-35.1467
200.9826-0.3327-0.93010.67640.27181.0635-0.2280.3342-0.2114-0.10920.16110.12570.1872-0.32910.14580.2972-0.04010.12030.95030.0790.3606-14.4849-110.1256-39.2933
210.5842-0.10140.39550.8352-0.39470.8079-0.0221-0.00440.0761-0.1556-0.02170.1585-0.0719-0.1156-0.07240.43620.2553-0.12740.6380.29190.4067-34.0967-60.7205-61.9787
223.17620.8684-0.033.5829-0.30921.31040.05060.2841-0.06710.08760.0640.12210.0208-0.15-0.06420.1659-0.0485-0.05250.87810.1110.2814-4.4013-95.5618-90.8025
232.1118-0.6964-0.35022.03780.61741.58960.047-0.34090.27930.24370.3525-0.36440.12480.2439-0.28580.45710.24-0.11940.76310.09210.653883.6109-108.311333.9721
242.51520.4492-0.40.9259-0.20471.46970.0607-0.12940.2407-0.0104-0.0164-0.27180.05630.1213-0.02220.35120.1034-0.13990.26340.09640.559684.6977-76.2905-8.3508
251.01970.2976-0.48660.78260.38460.65630.18980.35790.0779-0.5155-0.15350.23350.0214-0.2058-0.0420.9749-0.1981-0.14550.77740.44271.069725.4532-24.2893-41.7011
262.49810.9311-0.3011.15240.22922.3387-0.13330.29080.214-0.58930.2750.25970.1571-0.1285-0.13321.13240.1219-0.15361.47580.27430.4634-25.6203-58.9802-83.8158
273.670.05810.24832.1102-0.29871.8335-0.02650.0027-0.0966-0.0576-0.0715-0.24040.11990.05070.06430.27390.2192-0.05950.5433-0.03650.527169.2407-113.0149-14.9521
282.1482-0.2285-0.79890.8274-0.43280.6364-0.25070.5925-0.5026-0.07070.1090.07920.2968-0.3190.05780.3413-0.09480.2360.55870.02860.4724-13.7347-113.4705-24.4636
290.2989-0.07260.34770.2754-0.30850.59670.0007-0.0990.0133-0.01620.06890.136-0.1103-0.2651-0.10930.68240.1813-0.13230.88790.43410.5986-3.3908-54.6061-42.9786
300.1508-0.156-0.12280.19360.09960.1214-0.0277-0.04170.02750.00880.0238-0.0779-0.00820.09510.02810.2712-0.0577-0.0540.37460.27170.558964.1526-61.0137-33.3848
311.6826-0.9079-0.13811.9625-0.68921.12020.054-0.1686-0.06470.22250.01130.07250.0627-0.1185-0.03060.79610.1221-0.04110.89490.20.472835.8455-111.403843.1787
320.1597-0.0205-0.0130.3740.22030.1332-0.14060.00220.1272-0.26850.023-0.2683-0.26340.3057-0.11760.2767-0.07190.11250.69350.35210.436164.1062-69.6941-53.7032
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 2920 )X0
6X-RAY DIFFRACTION6chain 'Y' and (resid 1 through 114 )Y0
7X-RAY DIFFRACTION7chain 'A' and (resid 3 through 273 )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 170 )D0
11X-RAY DIFFRACTION11chain 'E' and (resid 18 through 173 )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 136 )J0
15X-RAY DIFFRACTION15chain 'K' and (resid 4 through 122 )K0
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 110 )L0
17X-RAY DIFFRACTION17chain 'M' and (resid 2 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 2 through 110 )P0
21X-RAY DIFFRACTION21chain 'Q' and (resid 2 through 90 )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 93 )T0
25X-RAY DIFFRACTION25chain 'U' and (resid 12 through 55 )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 43 )Z0
29X-RAY DIFFRACTION29chain '2' and (resid 2 through 45 )20
30X-RAY DIFFRACTION30chain '3' and (resid 2 through 61 )30
31X-RAY DIFFRACTION31chain '4' and (resid 1 through 37 )40
32X-RAY DIFFRACTION32chain 'I' and (resid 1 through 131 )I0

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