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- PDB-2hyb: Crystal Structure of Hexameric DsrEFH -

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Basic information

Entry
Database: PDB / ID: 2hyb
TitleCrystal Structure of Hexameric DsrEFH
Components
  • DsrH
  • Intracellular sulfur oxidation protein dsrF
  • Putative sulfurtransferase dsrE
KeywordsTRANSFERASE / DsrE / DsrF / DsrH / Sulfur / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


Transferases; Transferring sulfur-containing groups; Sulfurtransferases / sulfurtransferase complex / sulfur oxidation / tRNA wobble position uridine thiolation / sulfurtransferase activity / sulfur carrier activity
Similarity search - Function
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
Putative sulfurtransferase DsrE / Intracellular sulfur oxidation protein DsrF / DsrH
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsShin, D.H. / Connie, H. / Schulte, A. / Dahl, C. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: To be Published
Title: Crystal structure of hexameric DsrEFH
Authors: Shin, D.H. / Connie, H. / Schulte, A. / Dahl, C. / Kim, R. / Kim, S.H.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sulfurtransferase dsrE
B: Intracellular sulfur oxidation protein dsrF
C: DsrH
D: Putative sulfurtransferase dsrE
E: Intracellular sulfur oxidation protein dsrF
F: DsrH
G: Putative sulfurtransferase dsrE
H: Intracellular sulfur oxidation protein dsrF
I: DsrH
J: Putative sulfurtransferase dsrE
K: Intracellular sulfur oxidation protein dsrF
L: DsrH
M: Putative sulfurtransferase dsrE
N: Intracellular sulfur oxidation protein dsrF
O: DsrH
P: Putative sulfurtransferase dsrE
Q: Intracellular sulfur oxidation protein dsrF
R: DsrH


Theoretical massNumber of molelcules
Total (without water)247,85018
Polymers247,85018
Non-polymers00
Water7,530418
1
A: Putative sulfurtransferase dsrE
B: Intracellular sulfur oxidation protein dsrF
C: DsrH
D: Putative sulfurtransferase dsrE
E: Intracellular sulfur oxidation protein dsrF
F: DsrH


Theoretical massNumber of molelcules
Total (without water)82,6176
Polymers82,6176
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15810 Å2
ΔGint-44 kcal/mol
Surface area23790 Å2
MethodPISA
2
G: Putative sulfurtransferase dsrE
H: Intracellular sulfur oxidation protein dsrF
I: DsrH
J: Putative sulfurtransferase dsrE
K: Intracellular sulfur oxidation protein dsrF
L: DsrH


Theoretical massNumber of molelcules
Total (without water)82,6176
Polymers82,6176
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15820 Å2
ΔGint-43 kcal/mol
Surface area23750 Å2
MethodPISA
3
M: Putative sulfurtransferase dsrE
N: Intracellular sulfur oxidation protein dsrF
O: DsrH
P: Putative sulfurtransferase dsrE
Q: Intracellular sulfur oxidation protein dsrF
R: DsrH


Theoretical massNumber of molelcules
Total (without water)82,6176
Polymers82,6176
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15810 Å2
ΔGint-45 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.610, 183.110, 107.830
Angle α, β, γ (deg.)90.00, 99.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative sulfurtransferase dsrE / Intracellular sulfur oxidation protein dsrE


Mass: 14607.287 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: dsrE / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O87896, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#2: Protein
Intracellular sulfur oxidation protein dsrF


Mass: 15606.442 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: dsrF / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87897
#3: Protein
DsrH


Mass: 11094.615 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: dsrH / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87898
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20mg/ml protein, 0.1M Bis-Tris pH5.5 0.2M Lithium Sulfate 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. all: 74225 / Num. obs: 72592 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.3 Å2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 81.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 62422.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 6978 10.1 %RANDOM
Rwork0.206 ---
all0.211 72592 --
obs0.206 68871 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.7916 Å2 / ksol: 0.295294 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å21.67 Å2
2--0.71 Å20 Å2
3----3.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17193 0 0 418 17611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 911 10 %
Rwork0.312 8183 -
obs--73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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