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- PDB-6ny6: Structure of dimeric Escherichia coli toxin YoeB bound to the The... -

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Basic information

Entry
Database: PDB / ID: 6ny6
TitleStructure of dimeric Escherichia coli toxin YoeB bound to the Thermus thermophilus 30S ribosome
Components
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
  • Toxin YoeB
KeywordsRIBOSOME
Function / homology
Function and homology information


global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / RNA catabolic process / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters ...global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / RNA catabolic process / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters / small ribosomal subunit / response to heat / endonuclease activity / tRNA binding / Hydrolases; Acting on ester bonds / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 ...Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, type Z / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Few Secondary Structures / Irregular / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Toxin YoeB / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 ...IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Toxin YoeB / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Toxin YoeB / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.74 Å
AuthorsPavelich, I.J. / Hoffer, E.D. / Maehigashi, T. / Dunham, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 0953714 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093278 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
Authors: Pavelich, I.J. / Maehigashi, T. / Hoffer, E.D. / Ruangprasert, A. / Miles, S.J. / Dunham, C.M.
History
DepositionFeb 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein Thx
Y: Toxin YoeB
Z: Toxin YoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)809,056209
Polymers804,16723
Non-polymers4,889186
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)401.710, 401.710, 175.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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

#2: Protein 30S ribosomal protein S2 /


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3 /


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4 /


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#5: Protein 30S ribosomal protein S5 /


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7 /


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#8: Protein 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY9
#9: Protein 30S ribosomal protein S9 /


Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#10: Protein 30S ribosomal protein S10 /


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11 /


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12 /


Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: Protein 30S ribosomal protein S13 /


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY6
#15: Protein 30S ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16 /


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17 /


Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY7
#18: Protein 30S ribosomal protein S18 /


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19 /


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20 /


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Variant: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

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RNA chain / Protein , 2 types, 3 molecules AYZ

#1: RNA chain 16S rRNA /


Mass: 494263.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)
#22: Protein Toxin YoeB


Mass: 10233.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yoeB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A127GIW6, UniProt: P69348*PLUS

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Non-polymers , 3 types, 186 molecules

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


Mass: 24.305 Da / Num. of mol.: 184 / Source method: obtained synthetically / Formula: Mg
#24: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#25: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.44 Å3/Da / Density % sol: 72.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, AMMONIUM CHLORIDE, POTASSIUM CHLORIDE, MAGNESIUM ACETATE, SODIUM CACODYLATE, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.74→49.826 Å / Num. obs: 145546 / % possible obs: 96.9 % / Redundancy: 3.29 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06808 / Net I/σ(I): 10.95
Reflection shellResolution: 3.74→3.874 Å / Redundancy: 2.17 % / Rmerge(I) obs: 0.4847 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 9392 / CC1/2: 0.673 / % possible all: 85.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXdev_3406refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J5E

1j5e


Resolution: 3.74→49.826 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 7165 5 %
Rwork0.2057 --
obs0.2067 143162 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.74→49.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20542 32514 193 0 53249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857292
X-RAY DIFFRACTIONf_angle_d1.16384853
X-RAY DIFFRACTIONf_dihedral_angle_d22.85331455
X-RAY DIFFRACTIONf_chiral_restr0.05810612
X-RAY DIFFRACTIONf_plane_restr0.0075128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7401-3.78250.35572270.3433915X-RAY DIFFRACTION86
3.7825-3.8270.30621880.31614312X-RAY DIFFRACTION93
3.827-3.87370.28462210.29734427X-RAY DIFFRACTION96
3.8737-3.92270.29742480.29364523X-RAY DIFFRACTION98
3.9227-3.97430.27142300.2664614X-RAY DIFFRACTION100
3.9743-4.02870.26492520.27164543X-RAY DIFFRACTION100
4.0287-4.08620.25842690.26164591X-RAY DIFFRACTION100
4.0862-4.14720.27852340.25174593X-RAY DIFFRACTION99
4.1472-4.2120.28282520.24654592X-RAY DIFFRACTION100
4.212-4.2810.26122210.24564629X-RAY DIFFRACTION99
4.281-4.35480.27172700.24114520X-RAY DIFFRACTION99
4.3548-4.43390.24122320.23864549X-RAY DIFFRACTION98
4.4339-4.51910.24732640.22874516X-RAY DIFFRACTION98
4.5191-4.61130.22442330.22224590X-RAY DIFFRACTION99
4.6113-4.71150.25742270.21064615X-RAY DIFFRACTION99
4.7115-4.8210.23912130.2084607X-RAY DIFFRACTION99
4.821-4.94150.24292540.20714596X-RAY DIFFRACTION99
4.9415-5.0750.23732520.20254584X-RAY DIFFRACTION99
5.075-5.22410.22312120.19754630X-RAY DIFFRACTION99
5.2241-5.39260.22552290.19534583X-RAY DIFFRACTION99
5.3926-5.58510.21662310.19324516X-RAY DIFFRACTION97
5.5851-5.80840.20282390.1894618X-RAY DIFFRACTION99
5.8084-6.07230.24042130.19624608X-RAY DIFFRACTION98
6.0723-6.39180.20912420.19444574X-RAY DIFFRACTION98
6.3918-6.79130.23162570.19044547X-RAY DIFFRACTION97
6.7913-7.31420.19852470.18584547X-RAY DIFFRACTION96
7.3142-8.04750.22052380.17974532X-RAY DIFFRACTION96
8.0475-9.20560.20782620.1894520X-RAY DIFFRACTION96
9.2056-11.57410.16772460.17984471X-RAY DIFFRACTION93
11.5741-49.83040.19972620.18244535X-RAY DIFFRACTION91
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)
10.5269181012510.386520018846-0.2257031520630.7911361426990.006433937686710.587238991528-0.106994136885-0.113348736264-0.06947376324850.1385805519840.1193245710770.2772871759990.324212094733-0.0985870867984-0.01372559130961.25552055590.1145694492920.1992445450041.109743252320.1013132138191.49979797329121.6274617261.6511034915-5.71502745402
20.5474382295420.20695691861-0.1896104254910.756107181678-0.06571930385910.6657992932920.0428652512822-0.227670444471-0.07840389980680.4863627785480.09366732652570.2284929135610.1625948213550.124881522238-0.1303088361291.389405617630.1839471202020.1853453655821.223065671080.0178604736451.28967097033140.82919889287.16605739189.4413844474
31.65628907364-0.103883181175-0.6610943527030.5080000187170.2253463597920.983442450680.03548126973250.1551425594560.0885803446609-0.2566281414790.0858661723887-0.263058127418-0.01253220297580.328116807985-0.1225639341871.037539106890.05441654231720.1284890099291.13444098582-0.09471706328191.05115311948174.898629597106.406634921-50.3977123229
40.710059995169-0.2258671964310.09599826559680.317169363538-0.09927452105190.178758301743-0.00205151692398-0.7222763294110.1715802601350.3252639459360.0422255224238-0.0699746242984-0.2473327164060.17722666733-0.003914311294241.47914368863-0.1267844926180.1647024511612.23682599386-0.465440855921.57995745566211.83876232124.38171448115.5147980632
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1455.21235513613-0.06407375591471.908009707322.196723305982.163713145636.128425707420.1313508944790.1723692597540.989450486682-0.520798483943-1.42906227634-0.73463024102-0.9821230834281.144579815590.9583186433271.61588320167-0.167999336230.05573009183681.312746404530.6278955295942.0733397538699.390573387850.5959808048-35.2095053209
1460.00714117133964-0.0841071994309-0.05912580806933.19926588035-0.3215234940546.013137164760.05125403101880.109398520452-0.5966083239830.220175210654-0.2452820520711.218392788490.287717887711-1.208679230240.1685768370471.0813249672-0.2586696379450.3577357115923.30750307215-1.070780224072.88408287149251.335231446124.4610612982.54472471943
1471.10648171091-0.869802846761.197534526051.11025120288-0.08792178809383.00602987543-0.2771058290540.52758151131-0.0816810477021-0.6799647142950.04450221716390.0845707148094-0.06801536224890.3081118776670.2618610379912.564296114080.2030450107680.3070125745832.64431525815-1.480850111123.03079624096248.149733966129.4371703274.49345166833
1487.5559536069-0.346525317211-2.491793067130.01696086486420.1185049641190.818353254157-0.110610028341.46197711945-1.4353091754-0.221268943817-0.05354139291790.101445154131-0.302452483833-0.5262682077870.1239501849621.80225379304-0.270736379684-0.09595989826512.17771421536-0.562972452141.62694719674254.876223868133.83028765310.6445612088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 329 )
2X-RAY DIFFRACTION2chain 'A' and (resid 330 through 661 )
3X-RAY DIFFRACTION3chain 'A' and (resid 662 through 907 )
4X-RAY DIFFRACTION4chain 'A' and (resid 908 through 1142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1143 through 1382 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1383 through 1540 )
7X-RAY DIFFRACTION7chain 'Y' and (resid 1 through 6 )
8X-RAY DIFFRACTION8chain 'Y' and (resid 7 through 20 )
9X-RAY DIFFRACTION9chain 'Y' and (resid 21 through 36 )
10X-RAY DIFFRACTION10chain 'Y' and (resid 37 through 55 )
11X-RAY DIFFRACTION11chain 'Y' and (resid 56 through 64 )
12X-RAY DIFFRACTION12chain 'Y' and (resid 65 through 71 )
13X-RAY DIFFRACTION13chain 'Y' and (resid 72 through 78 )
14X-RAY DIFFRACTION14chain 'Y' and (resid 79 through 84 )
15X-RAY DIFFRACTION15chain 'Z' and (resid 1 through 20 )
16X-RAY DIFFRACTION16chain 'Z' and (resid 21 through 55 )
17X-RAY DIFFRACTION17chain 'Z' and (resid 56 through 84 )
18X-RAY DIFFRACTION18chain 'B' and (resid 5 through 28 )
19X-RAY DIFFRACTION19chain 'B' and (resid 29 through 120 )
20X-RAY DIFFRACTION20chain 'B' and (resid 121 through 136 )
21X-RAY DIFFRACTION21chain 'B' and (resid 137 through 219 )
22X-RAY DIFFRACTION22chain 'B' and (resid 220 through 240 )
23X-RAY DIFFRACTION23chain 'C' and (resid 2 through 28 )
24X-RAY DIFFRACTION24chain 'C' and (resid 29 through 49 )
25X-RAY DIFFRACTION25chain 'C' and (resid 50 through 62 )
26X-RAY DIFFRACTION26chain 'C' and (resid 63 through 93 )
27X-RAY DIFFRACTION27chain 'C' and (resid 94 through 112 )
28X-RAY DIFFRACTION28chain 'C' and (resid 113 through 125 )
29X-RAY DIFFRACTION29chain 'C' and (resid 126 through 171 )
30X-RAY DIFFRACTION30chain 'C' and (resid 172 through 206 )
31X-RAY DIFFRACTION31chain 'D' and (resid 2 through 15 )
32X-RAY DIFFRACTION32chain 'D' and (resid 16 through 35 )
33X-RAY DIFFRACTION33chain 'D' and (resid 36 through 68 )
34X-RAY DIFFRACTION34chain 'D' and (resid 69 through 83 )
35X-RAY DIFFRACTION35chain 'D' and (resid 84 through 148 )
36X-RAY DIFFRACTION36chain 'D' and (resid 149 through 163 )
37X-RAY DIFFRACTION37chain 'D' and (resid 164 through 185 )
38X-RAY DIFFRACTION38chain 'D' and (resid 186 through 199 )
39X-RAY DIFFRACTION39chain 'D' and (resid 200 through 209 )
40X-RAY DIFFRACTION40chain 'E' and (resid 5 through 35 )
41X-RAY DIFFRACTION41chain 'E' and (resid 36 through 50 )
42X-RAY DIFFRACTION42chain 'E' and (resid 51 through 64 )
43X-RAY DIFFRACTION43chain 'E' and (resid 65 through 79 )
44X-RAY DIFFRACTION44chain 'E' and (resid 80 through 103 )
45X-RAY DIFFRACTION45chain 'E' and (resid 104 through 112 )
46X-RAY DIFFRACTION46chain 'E' and (resid 113 through 141 )
47X-RAY DIFFRACTION47chain 'E' and (resid 142 through 155 )
48X-RAY DIFFRACTION48chain 'F' and (resid 1 through 15 )
49X-RAY DIFFRACTION49chain 'F' and (resid 16 through 32 )
50X-RAY DIFFRACTION50chain 'F' and (resid 33 through 47 )
51X-RAY DIFFRACTION51chain 'F' and (resid 48 through 67 )
52X-RAY DIFFRACTION52chain 'F' and (resid 68 through 80 )
53X-RAY DIFFRACTION53chain 'F' and (resid 81 through 100 )
54X-RAY DIFFRACTION54chain 'G' and (resid 2 through 11 )
55X-RAY DIFFRACTION55chain 'G' and (resid 12 through 35 )
56X-RAY DIFFRACTION56chain 'G' and (resid 36 through 52 )
57X-RAY DIFFRACTION57chain 'G' and (resid 53 through 69 )
58X-RAY DIFFRACTION58chain 'G' and (resid 70 through 92 )
59X-RAY DIFFRACTION59chain 'G' and (resid 93 through 109 )
60X-RAY DIFFRACTION60chain 'G' and (resid 110 through 115 )
61X-RAY DIFFRACTION61chain 'G' and (resid 116 through 129 )
62X-RAY DIFFRACTION62chain 'G' and (resid 130 through 156 )
63X-RAY DIFFRACTION63chain 'H' and (resid 2 through 19 )
64X-RAY DIFFRACTION64chain 'H' and (resid 20 through 29 )
65X-RAY DIFFRACTION65chain 'H' and (resid 30 through 63 )
66X-RAY DIFFRACTION66chain 'H' and (resid 64 through 85 )
67X-RAY DIFFRACTION67chain 'H' and (resid 86 through 102 )
68X-RAY DIFFRACTION68chain 'H' and (resid 103 through 119 )
69X-RAY DIFFRACTION69chain 'H' and (resid 120 through 130 )
70X-RAY DIFFRACTION70chain 'H' and (resid 131 through 138 )
71X-RAY DIFFRACTION71chain 'I' and (resid 2 through 12 )
72X-RAY DIFFRACTION72chain 'I' and (resid 13 through 32 )
73X-RAY DIFFRACTION73chain 'I' and (resid 33 through 42 )
74X-RAY DIFFRACTION74chain 'I' and (resid 43 through 58 )
75X-RAY DIFFRACTION75chain 'I' and (resid 59 through 84 )
76X-RAY DIFFRACTION76chain 'I' and (resid 85 through 96 )
77X-RAY DIFFRACTION77chain 'I' and (resid 97 through 106 )
78X-RAY DIFFRACTION78chain 'I' and (resid 107 through 121 )
79X-RAY DIFFRACTION79chain 'I' and (resid 122 through 127 )
80X-RAY DIFFRACTION80chain 'J' and (resid 5 through 12 )
81X-RAY DIFFRACTION81chain 'J' and (resid 13 through 28 )
82X-RAY DIFFRACTION82chain 'J' and (resid 29 through 37 )
83X-RAY DIFFRACTION83chain 'J' and (resid 38 through 42 )
84X-RAY DIFFRACTION84chain 'J' and (resid 43 through 60 )
85X-RAY DIFFRACTION85chain 'J' and (resid 61 through 72 )
86X-RAY DIFFRACTION86chain 'J' and (resid 73 through 84 )
87X-RAY DIFFRACTION87chain 'J' and (resid 85 through 94 )
88X-RAY DIFFRACTION88chain 'J' and (resid 95 through 100 )
89X-RAY DIFFRACTION89chain 'K' and (resid 11 through 23 )
90X-RAY DIFFRACTION90chain 'K' and (resid 24 through 34 )
91X-RAY DIFFRACTION91chain 'K' and (resid 35 through 43 )
92X-RAY DIFFRACTION92chain 'K' and (resid 44 through 57 )
93X-RAY DIFFRACTION93chain 'K' and (resid 58 through 72 )
94X-RAY DIFFRACTION94chain 'K' and (resid 73 through 78 )
95X-RAY DIFFRACTION95chain 'K' and (resid 79 through 90 )
96X-RAY DIFFRACTION96chain 'K' and (resid 91 through 99 )
97X-RAY DIFFRACTION97chain 'K' and (resid 100 through 110 )
98X-RAY DIFFRACTION98chain 'K' and (resid 111 through 120 )
99X-RAY DIFFRACTION99chain 'K' and (resid 121 through 126 )
100X-RAY DIFFRACTION100chain 'L' and (resid 5 through 12 )
101X-RAY DIFFRACTION101chain 'L' and (resid 13 through 22 )
102X-RAY DIFFRACTION102chain 'L' and (resid 23 through 32 )
103X-RAY DIFFRACTION103chain 'L' and (resid 33 through 69 )
104X-RAY DIFFRACTION104chain 'L' and (resid 70 through 81 )
105X-RAY DIFFRACTION105chain 'L' and (resid 82 through 110 )
106X-RAY DIFFRACTION106chain 'L' and (resid 111 through 126 )
107X-RAY DIFFRACTION107chain 'M' and (resid 2 through 14 )
108X-RAY DIFFRACTION108chain 'M' and (resid 15 through 49 )
109X-RAY DIFFRACTION109chain 'M' and (resid 50 through 66 )
110X-RAY DIFFRACTION110chain 'M' and (resid 67 through 81 )
111X-RAY DIFFRACTION111chain 'M' and (resid 82 through 107 )
112X-RAY DIFFRACTION112chain 'M' and (resid 108 through 117 )
113X-RAY DIFFRACTION113chain 'N' and (resid 2 through 11 )
114X-RAY DIFFRACTION114chain 'N' and (resid 12 through 29 )
115X-RAY DIFFRACTION115chain 'N' and (resid 30 through 39 )
116X-RAY DIFFRACTION116chain 'N' and (resid 40 through 44 )
117X-RAY DIFFRACTION117chain 'N' and (resid 45 through 61 )
118X-RAY DIFFRACTION118chain 'O' and (resid 2 through 24 )
119X-RAY DIFFRACTION119chain 'O' and (resid 25 through 49 )
120X-RAY DIFFRACTION120chain 'O' and (resid 50 through 73 )
121X-RAY DIFFRACTION121chain 'O' and (resid 74 through 88 )
122X-RAY DIFFRACTION122chain 'P' and (resid 1 through 36 )
123X-RAY DIFFRACTION123chain 'P' and (resid 37 through 48 )
124X-RAY DIFFRACTION124chain 'P' and (resid 49 through 62 )
125X-RAY DIFFRACTION125chain 'P' and (resid 63 through 84 )
126X-RAY DIFFRACTION126chain 'Q' and (resid 2 through 12 )
127X-RAY DIFFRACTION127chain 'Q' and (resid 13 through 34 )
128X-RAY DIFFRACTION128chain 'Q' and (resid 35 through 70 )
129X-RAY DIFFRACTION129chain 'Q' and (resid 71 through 101 )
130X-RAY DIFFRACTION130chain 'R' and (resid 19 through 24 )
131X-RAY DIFFRACTION131chain 'R' and (resid 25 through 36 )
132X-RAY DIFFRACTION132chain 'R' and (resid 37 through 43 )
133X-RAY DIFFRACTION133chain 'R' and (resid 44 through 52 )
134X-RAY DIFFRACTION134chain 'R' and (resid 53 through 59 )
135X-RAY DIFFRACTION135chain 'R' and (resid 60 through 76 )
136X-RAY DIFFRACTION136chain 'R' and (resid 77 through 88 )
137X-RAY DIFFRACTION137chain 'S' and (resid 2 through 15 )
138X-RAY DIFFRACTION138chain 'S' and (resid 16 through 30 )
139X-RAY DIFFRACTION139chain 'S' and (resid 31 through 41 )
140X-RAY DIFFRACTION140chain 'S' and (resid 42 through 47 )
141X-RAY DIFFRACTION141chain 'S' and (resid 48 through 52 )
142X-RAY DIFFRACTION142chain 'S' and (resid 53 through 85 )
143X-RAY DIFFRACTION143chain 'T' and (resid 8 through 12 )
144X-RAY DIFFRACTION144chain 'T' and (resid 13 through 75 )
145X-RAY DIFFRACTION145chain 'T' and (resid 76 through 106 )
146X-RAY DIFFRACTION146chain 'U' and (resid 2 through 8 )
147X-RAY DIFFRACTION147chain 'U' and (resid 9 through 15 )
148X-RAY DIFFRACTION148chain 'U' and (resid 16 through 26 )

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