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

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Basic information

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


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / 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, / Helix Hairpins - #310 / Ribosomal Protein L25; Chain P / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / 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, / Helix Hairpins - #310 / Ribosomal Protein L25; Chain P / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / 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 L14 / Ribosomal protein L14/L23 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L30; Chain: A, / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / 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 L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Beta Complex / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L28 family / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Few Secondary Structures
Similarity search - Domain/homology
ETHANOL / : / SPERMIDINE / Chem-ZLD / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 ...ETHANOL / : / SPERMIDINE / Chem-ZLD / : / 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
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.392 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 / _diffrn_radiation_wavelength.wavelength / _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 1.4Nov 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
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)1,362,368498
Polymers1,341,76128
Non-polymers20,607470
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area134850 Å2
ΔGint-1258 kcal/mol
Surface area462130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.922, 279.922, 870.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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


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


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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain USA300) (bacteria)
Strain: USA300 / References: UniProt: Q2FJE0
#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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (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 (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW29

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Non-polymers , 8 types, 470 molecules

#29: Chemical ChemComp-ZLD / N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide / Linezolid


Mass: 337.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20FN3O4
#30: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#31: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 246 / Source method: obtained synthetically / Formula: Mg
#32: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 195 / Source method: obtained synthetically / Formula: Mn
#33: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#34: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


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


Mass: 145.246 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C7H19N3
#36: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O

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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: 3.67 Å3/Da / Density % sol: 66.48 %
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: ID23-1 / Wavelength: 0.873,0.972,1.000
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8731
20.9721
311
ReflectionResolution: 3.4→200 Å / Num. obs: 246474 / % possible obs: 89.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 109.33 Å2 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.061 / Rrim(I) all: 0.17 / Χ2: 1.171 / Net I/av σ(I): 8.45 / Net I/σ(I): 5.7 / Num. measured all: 1398748
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.462.80.77688640.4330.4190.8951.21464.8
3.46-3.523.30.75595720.5060.3680.8531.20970.7
3.52-3.594.40.775111650.5550.3380.8571.21782
3.59-3.6650.713117770.6030.2910.781.21986.7
3.66-3.745.60.627123860.7570.2430.6811.22290.7
3.74-3.835.80.597126560.7210.2320.6491.25493
3.83-3.935.60.491126910.7730.1940.5351.20293.2
3.93-4.036.10.446126960.8150.1670.4821.21393
4.03-4.156.40.386127630.8610.1410.4161.21493.3
4.15-4.286.30.334127670.8870.1230.3611.24893.3
4.28-4.446.20.288127770.9230.1060.3111.2393.2
4.44-4.616.10.244128130.9330.0920.2631.22693.5
4.61-4.825.70.216127890.9370.0850.2361.20192.9
4.82-5.086.10.185128410.9590.0690.21.17993.3
5.08-5.46.40.159128510.9680.0580.1721.12193
5.4-5.816.30.142128890.9740.0530.1541.09493.3
5.81-6.45.80.127130400.9780.0510.1391.07393.6
6.4-7.326.20.108129970.9840.0410.1171.0692.9
7.32-9.2360.093130150.9880.0360.1011.06192
9.23-2005.60.07131250.9960.0290.0771.05388.2

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Processing

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

4wce


Resolution: 3.392→64.877 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 12430 5.06 %Random selection
Rwork0.2018 ---
obs0.2038 245559 88.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.392→64.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20181 60581 703 0 81465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00688500
X-RAY DIFFRACTIONf_angle_d1.086133771
X-RAY DIFFRACTIONf_dihedral_angle_d16.97840888
X-RAY DIFFRACTIONf_chiral_restr0.05817470
X-RAY DIFFRACTIONf_plane_restr0.0066515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3922-3.43070.33842770.30735036X-RAY DIFFRACTION59
3.4307-3.47110.33052830.29545787X-RAY DIFFRACTION67
3.4711-3.51340.33753070.28815967X-RAY DIFFRACTION69
3.5134-3.55790.32033930.29076952X-RAY DIFFRACTION81
3.5579-3.60470.31713900.28077047X-RAY DIFFRACTION82
3.6047-3.65410.29344090.26637543X-RAY DIFFRACTION87
3.6541-3.70630.29084230.25287641X-RAY DIFFRACTION89
3.7063-3.76160.29254290.24498067X-RAY DIFFRACTION93
3.7616-3.82040.2864230.23828000X-RAY DIFFRACTION93
3.8204-3.8830.26234400.23318064X-RAY DIFFRACTION93
3.883-3.94990.27334300.22788029X-RAY DIFFRACTION93
3.9499-4.02180.25464600.21517977X-RAY DIFFRACTION93
4.0218-4.09910.25844200.2128141X-RAY DIFFRACTION94
4.0991-4.18280.23224660.20218063X-RAY DIFFRACTION93
4.1828-4.27370.24074330.19888063X-RAY DIFFRACTION93
4.2737-4.37310.25324700.19698088X-RAY DIFFRACTION93
4.3731-4.48240.24194250.18368110X-RAY DIFFRACTION93
4.4824-4.60360.2254210.18058114X-RAY DIFFRACTION93
4.6036-4.7390.21534350.17688110X-RAY DIFFRACTION93
4.739-4.89190.23564150.17378136X-RAY DIFFRACTION93
4.8919-5.06670.21594290.16658117X-RAY DIFFRACTION93
5.0667-5.26950.21334260.16398196X-RAY DIFFRACTION93
5.2695-5.50920.23284360.17028127X-RAY DIFFRACTION93
5.5092-5.79950.20944100.16268206X-RAY DIFFRACTION93
5.7995-6.16260.2224310.16828265X-RAY DIFFRACTION94
6.1626-6.63790.22874300.17118262X-RAY DIFFRACTION93
6.6379-7.30510.20284090.16418244X-RAY DIFFRACTION93
7.3051-8.36030.21224090.17568271X-RAY DIFFRACTION92
8.3603-10.52580.23194630.19028234X-RAY DIFFRACTION91
10.5258-64.88840.25564380.2458272X-RAY DIFFRACTION87
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)
10.4812-0.1263-0.03810.2183-0.00920.4489-0.09060.6160.3114-0.1584-0.0158-0.1095-0.2371-0.08890.09260.66050.0052-0.05921.13920.59950.676522.2777-64.0005-59.8725
20.4396-0.0699-0.08510.29520.13860.1678-0.05840.06820.24590.05940.0179-0.0309-0.2637-0.04780.05430.70390.1779-0.02590.63720.26360.6820.8175-64.1348-7.485
30.682-0.1139-0.14970.32460.07970.3242-0.0930.1940.18130.04560.02610.0176-0.1666-0.17330.07330.57960.21240.0130.74290.22080.5092-3.7049-76.1309-17.0544
40.40660.1177-0.08170.23020.03320.3402-0.1584-0.20160.64680.01630.0632-0.0145-0.21820.13170.13211.15010.2698-0.17510.69150.0231.259815.9172-36.45660.8079
50.63880.0151-0.0610.27-0.03920.3401-0.1462-0.15040.15510.23530.0448-0.0795-0.1322-0.09140.09010.59040.2219-0.03010.59440.08990.506318.7525-82.07962.7871
60.2634-0.2088-0.02260.2476-0.20390.4722-0.178-0.16430.27330.12740.1101-0.2975-0.10050.27820.01790.7868-0.0156-0.30510.95680.01191.1416103.0138-81.024415.1924
70.0820.06960.01420.0759-0.008-0.00970.1473-0.0390.12980.0131-0.01290.035-0.2151-0.17530.00130.97540.3025-0.07960.4260.21731.2519-6.0503-17.5048-11.8413
80.38730.0168-0.07070.587-0.07660.28970.0105-0.0733-0.06810.18260.03620.09920.0202-0.1409-0.01570.57180.1830.31160.79640.14810.6599-18.193-121.122314.2461
90.1880.0865-0.17420.085-0.0970.4181-0.06160.41510.04880.0271-0.01810.0001-0.06650.0126-0.17610.6482-0.13560.11631.2870.40330.606240.2652-84.647-72.0332
100.4931-0.36030.24110.2943-0.2320.19830.2255-0.3894-0.0840.4710.0714-0.2271-0.13990.1493-0.040.95880.0526-0.36390.9283-0.35451.0111104.8713-49.392636.5315
110.4251-0.2061-0.33770.62320.20570.4761-0.09850.0436-0.14290.1593-0.01970.14020.1893-0.03310.05620.99660.19410.10611.14420.48481.294725.0769-134.632951.7675
120.3575-0.10430.03190.5259-0.12590.2362-0.0849-0.0709-0.22360.18690.03070.01170.0086-0.19070.00410.610.13850.21580.60490.17530.696922.6654-136.00852.6523
131.03530.3251-0.05740.614-0.03640.8517-0.1101-0.18360.12240.2693-0.04730.06870.0708-0.240.05410.99150.27530.11971.1639-0.02660.4848-19.7243-85.608941.0855
140.05380.0353-0.05270.031-0.02780.0555-0.12070.11090.0221-0.2263-0.0013-0.1075-0.1280.16110.01820.4604-0.03560.0910.74170.33550.696963.9497-69.1504-53.2839
150.50650.08490.34341.397-0.87492.2499-0.0821-0.4385-0.04580.312-0.1694-0.11290.11630.21940.10080.82250.1482-0.20030.96430.05820.584858.3973-89.252131.1166
161.3433-0.0186-0.74810.83050.26570.7243-0.02370.0942-0.0520.08180.02250.1492-0.0142-0.38810.01230.32670.08210.18990.68570.01620.533-47.3379-101.5859-13.805
170.187-0.1933-0.13660.20610.24071.2285-0.0627-0.0839-0.02140.0592-0.0255-0.07470.0283-0.07140.00360.6324-0.0437-0.09480.56690.02321.1429117.7154-65.1481-0.6855
181.0216-0.4368-0.64891.34490.4330.9535-0.082-0.0964-0.06980.1196-0.04750.11580.0616-0.0364-0.09840.64260.26070.37330.8949-0.02170.5343-42.1473-98.526232.7315
190.5965-0.40150.14440.7526-0.15150.4385-0.1120.1477-0.06770.07960.0107-0.05690.0936-0.06580.01380.30580.05310.22550.53670.10870.488636.0214-126.3833-23.3156
200.4873-0.4862-0.07481.25690.150.4604-0.09490.2268-0.1603-0.1288-0.0115-0.05740.22070.15040.00570.59240.13590.19580.65080.01310.537544.4512-134.1224-34.9758
211.22180.32730.22981.36370.28391.3459-0.14380.175-0.1396-0.14090.0824-0.00980.08380.04630.01830.43060.00010.16040.81330.05960.4213-14.0543-110.6234-39.5727
221.36530.03570.3411.0022-0.27051.31650.08130.13360.1291-0.0922-0.10850.1459-0.0441-0.10140.01870.90720.18-0.1671.38190.4630.9442-33.7136-60.3775-61.5316
232.49940.2685-0.87012.1918-0.05512.3884-0.01520.43230.1058-0.20620.1549-0.1419-0.0681-0.0252-0.10890.5355-0.06380.03971.05770.14030.5744-4.5797-95.3801-89.7716
241.43460.12010.13220.93310.10511.46710.1284-0.17560.41180.19070.0047-0.0646-0.0421-0.0045-0.09240.63940.1161-0.15950.78770.03260.785183.3215-106.577235.1662
251.38810.5366-0.03590.5105-0.25910.7682-0.071-0.13490.11720.0576-0.1619-0.33720.13150.23860.01890.88110.059-0.1350.79590.23740.933884.5935-75.8814-8.1724
260.42520.20290.02370.12780.04920.06780.07620.13250.1084-0.26490.04140.3407-0.1327-0.3064-0.10071.35530.0005-0.24991.1330.27551.410525.484-24.0095-41.491
272.17680.1402-0.62350.9848-0.25522.5318-0.21150.21290.1593-0.1724-0.04770.0457-0.00390.01150.02561.0260.1666-0.16311.18790.23120.5415-24.5356-58.5836-83.7785
282.75880.12370.12451.18030.41161.7842-0.05080.0151-0.23260.01390.0405-0.14250.12690.09510.00350.2973-0.0350.0430.45780.04710.576369.2598-112.7365-15.0654
290.4192-0.2762-0.43330.8561-0.15270.754-0.15820.2216-0.2273-0.06410.21140.13930.3152-0.2379-0.00960.41560.03720.15620.4790.07780.5116-13.8919-112.9226-24.4866
300.2703-0.0351-0.04480.3872-0.16680.32640.03390.05030.0442-0.02450.03680.1184-0.1398-0.1755-0.11550.66150.1295-0.12780.84950.40730.6846-3.0296-54.4585-43.2231
310.80890.04750.09210.54610.08080.0617-0.0491-0.00460.0771-0.01990.1327-0.14230.10090.0835-0.02980.4574-0.0831-0.19370.51250.28460.595464.0984-60.4544-32.9335
322.4282-0.6865-0.21841.7447-0.41072.48510.0336-0.12060.08690.18110.0506-0.0509-0.0770.052-0.00021.42910.1909-0.00771.380.16060.846436.0712-111.024243.3123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'X' and (resid 1 through 722 )
2X-RAY DIFFRACTION2chain 'X' and (resid 723 through 948 )
3X-RAY DIFFRACTION3chain 'X' and (resid 949 through 1790 )
4X-RAY DIFFRACTION4chain 'X' and (resid 1791 through 2021 )
5X-RAY DIFFRACTION5chain 'X' and (resid 2022 through 2920 )
6X-RAY DIFFRACTION6chain 'Y' and (resid 1 through 114 )
7X-RAY DIFFRACTION7chain 'A' and (resid 3 through 271 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 216 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 201 )
10X-RAY DIFFRACTION10chain 'D' and (resid 7 through 179 )
11X-RAY DIFFRACTION11chain 'E' and (resid 17 through 173 )
12X-RAY DIFFRACTION12chain 'G' and (resid 3 through 142)
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 122 )
14X-RAY DIFFRACTION14chain 'I' and (resid 1 through 131 )
15X-RAY DIFFRACTION15chain 'J' and (resid 4 through 141 )
16X-RAY DIFFRACTION16chain 'K' and (resid 4 through 122 )
17X-RAY DIFFRACTION17chain 'L' and (resid 4 through 111 )
18X-RAY DIFFRACTION18chain 'M' and (resid 2 through 110 )
19X-RAY DIFFRACTION19chain 'N' and (resid 2 through 117 )
20X-RAY DIFFRACTION20chain 'O' and (resid 1 through 101 )
21X-RAY DIFFRACTION21chain 'P' and (resid 1 through 112 )
22X-RAY DIFFRACTION22chain 'Q' and (resid 2 through 91 )
23X-RAY DIFFRACTION23chain 'R' and (resid 3 through 102 )
24X-RAY DIFFRACTION24chain 'S' and (resid 3 through 169 )
25X-RAY DIFFRACTION25chain 'T' and (resid 19 through 93 )
26X-RAY DIFFRACTION26chain 'U' and (resid 12 through 55 )
27X-RAY DIFFRACTION27chain 'V' and (resid 2 through 66 )
28X-RAY DIFFRACTION28chain 'W' and (resid 2 through 58 )
29X-RAY DIFFRACTION29chain 'Z' and (resid 2 through 45 )
30X-RAY DIFFRACTION30chain '2' and (resid 2 through 45 )
31X-RAY DIFFRACTION31chain '3' and (resid 2 through 61 )
32X-RAY DIFFRACTION32chain '4' and (resid 1 through 37 )

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