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- PDB-3eqe: Crystal structure of the YubC protein from Bacillus subtilis. Nor... -

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Basic information

Entry
Database: PDB / ID: 3eqe
TitleCrystal structure of the YubC protein from Bacillus subtilis. Northeast Structural Genomics Consortium target SR112.
ComponentsPutative cystein dioxygenase
KeywordsOXIDOREDUCTASE / Cystein dioxygenase / YubC / SR112 / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


cysteine dioxygenase / cysteine dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding
Similarity search - Function
Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Cysteine dioxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Benach, J. / Forouhar, F. / Clayton, G. / Cooper, B. / Wang, H. / Foote, E.L. / Ciccosanti, C. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Benach, J. / Forouhar, F. / Clayton, G. / Cooper, B. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the YubC protein from Bacillus subtilis.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Benach, J. / Forouhar, F. / Clayton, G. / Cooper, B. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G. ...Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Benach, J. / Forouhar, F. / Clayton, G. / Cooper, B. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cystein dioxygenase
B: Putative cystein dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4524
Polymers39,3412
Non-polymers1122
Water1,15364
1
A: Putative cystein dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7262
Polymers19,6701
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cystein dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7262
Polymers19,6701
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.830, 65.830, 197.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

DetailsAUTHORS STATE THAT THE OLIGOMERIC STATE OF THE YUBC PROTEIN IS A MONOMER ACCORDING TO GEL-FILTRATION AND AGGREGATION ANALYSIS.

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Components

#1: Protein Putative cystein dioxygenase


Mass: 19670.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU31140, yubC / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O32085, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 4000, 0.1M KAcetate, 0.05M MES, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. all: 20159 / Num. obs: 19930 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.24 % / Biso Wilson estimate: 99.6 Å2 / Rmerge(I) obs: 0.0857 / Net I/σ(I): 22.89
Reflection shellResolution: 2.82→2.95 Å / Redundancy: 9.84 % / Rmerge(I) obs: 0.6328 / Mean I/σ(I) obs: 3.58 / Num. unique all: 2657 / % possible all: 92.3

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Processing

Software
NameVersionClassification
SHELXDEphasing
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.82→46.51 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 228392.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.296 465 4.2 %RANDOM
Rwork0.241 ---
obs0.241 11098 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.5048 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 69.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.4 Å20 Å20 Å2
2--9.4 Å20 Å2
3----18.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.82→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 2 64 2446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
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: 2.82→3 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 66 3.7 %
Rwork0.334 1695 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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