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- PDB-2d1p: crystal structure of heterohexameric TusBCD proteins, which are c... -

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Basic information

Entry
Database: PDB / ID: 2d1p
Titlecrystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification
Components
  • Hypothetical UPF0116 protein yheM
  • Hypothetical UPF0163 protein yheN
  • Hypothetical protein yheLHypothesis
KeywordsTRANSLATION / tRNA modification / sulfur transfer / Structural genomics
Function / homology
Function and homology information


sulfurtransferase complex / Transferases; Transferring sulfur-containing groups; Sulfurtransferases / sulfur carrier activity / tRNA wobble position uridine thiolation / sulfurtransferase activity / cytosol
Similarity search - Function
Sulphur relay, TusB / Sulphur relay, TusC / Sulphur relay, TusC/DsrF / Sulphur relay, TusD/DsrE / Sulphur relay, TusB/DsrH / DsrH like protein / Sulphur relay, DsrE/F-like / DsrE/DsrF-like family / DsrEFH-like / DsrEFH-like ...Sulphur relay, TusB / Sulphur relay, TusC / Sulphur relay, TusC/DsrF / Sulphur relay, TusD/DsrE / Sulphur relay, TusB/DsrH / DsrH like protein / Sulphur relay, DsrE/F-like / DsrE/DsrF-like family / DsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein TusB / Protein TusC / Sulfurtransferase TusD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsNumata, T. / Fukai, S. / Ikeuchi, Y. / Suzuki, T. / Nureki, O.
CitationJournal: Structure / Year: 2006
Title: Structural Basis for Sulfur Relay to RNA Mediated by Heterohexameric TusBCD Complex
Authors: Numata, T. / Fukai, S. / Ikeuchi, Y. / Suzuki, T. / Nureki, O.
History
DepositionAug 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical UPF0163 protein yheN
B: Hypothetical UPF0116 protein yheM
C: Hypothetical protein yheL
D: Hypothetical UPF0163 protein yheN
E: Hypothetical UPF0116 protein yheM
F: Hypothetical protein yheL
G: Hypothetical UPF0163 protein yheN
H: Hypothetical UPF0116 protein yheM
I: Hypothetical protein yheL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,62210
Polymers116,5269
Non-polymers961
Water5,116284
1
A: Hypothetical UPF0163 protein yheN
B: Hypothetical UPF0116 protein yheM
C: Hypothetical protein yheL

A: Hypothetical UPF0163 protein yheN
B: Hypothetical UPF0116 protein yheM
C: Hypothetical protein yheL


Theoretical massNumber of molelcules
Total (without water)77,6846
Polymers77,6846
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area15010 Å2
ΔGint-58 kcal/mol
Surface area22900 Å2
MethodPISA
2
D: Hypothetical UPF0163 protein yheN
E: Hypothetical UPF0116 protein yheM
F: Hypothetical protein yheL
G: Hypothetical UPF0163 protein yheN
H: Hypothetical UPF0116 protein yheM
I: Hypothetical protein yheL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7807
Polymers77,6846
Non-polymers961
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-69 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.392, 141.392, 135.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hypothetical UPF0163 protein yheN / TusD


Mass: 15055.728 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yheN / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P45532
#2: Protein Hypothetical UPF0116 protein yheM / TusC


Mass: 13056.959 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yheM / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P45531
#3: Protein Hypothetical protein yheL / Hypothesis / TusB


Mass: 10729.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yheL / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P45530
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.9-1.1M lithium sulfate, 9mM Mg-acetate, 45mM Na-cacodylate buffer (pH 6.8), 2.5% tert-butanol, and 10mM Tris-HCl buffer (pH8.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979521, 0.979829, 0.9830
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2004 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795211
20.9798291
30.9831
ReflectionResolution: 2.15→50 Å / Num. obs: 74991 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 43.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 7.1 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.15→50 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Rfactor% reflectionSelection details
Rfree0.2423 -RANDOM
Rwork0.2094 --
obs0.2094 99.7 %-
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.11 Å20 Å20 Å2
2---4.11 Å20 Å2
3---8.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7925 0 5 284 8214
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.006 /
Rfactor% reflection
Rfree0.274 -
Rwork0.25 -
obs-99.4 %

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