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- PDB-4hc5: Crystal structure of member of Glyoxalase/bleomycin resistance pr... -

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Basic information

Entry
Database: PDB / ID: 4hc5
TitleCrystal structure of member of Glyoxalase/bleomycin resistance protein/dioxygenase superfamily from Sphaerobacter thermophilus DSM 20745
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsOXIDOREDUCTASE / MCSG / GEBA genomes / Structural Genomics / Midwest Center for Structural Genomics / pfam00903 / PSI-Biology
Function / homology
Function and homology information


dioxygenase activity
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Glyoxalase/bleomycin resistance protein/dioxygenase
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsNocek, B. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of member of Glyoxalase/bleomycin resistance protein/dioxygenase superfamily from Sphaerobacter thermophilus DSM 20745
Authors: Nocek, B. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
C: Glyoxalase/bleomycin resistance protein/dioxygenase
D: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0056
Polymers60,8214
Non-polymers1842
Water9,908550
1
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5954
Polymers30,4112
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-29 kcal/mol
Surface area11750 Å2
MethodPISA
2
C: Glyoxalase/bleomycin resistance protein/dioxygenase
D: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)30,4112
Polymers30,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-26 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.883, 71.023, 86.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 15205.323 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / Gene: Sthe_2956 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: D1C967
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium sulfate 1.5 M, Tris 0.1 M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2012 / Details: mirrors
RadiationMonochromator: double crysta / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.45→86 Å / Num. all: 116629 / Num. obs: 115474 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 40
Reflection shellResolution: 1.45→1.48 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→26.59 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.951 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.053 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE ARE UNMODEL DENSITY FEATURES OBSERVED IN THE POCKET FORMED BY RESIDUES (F38, F48, W110, F126). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18271 5757 5 %RANDOM
Rwork0.13691 ---
obs0.1391 109125 98.41 %-
all-114882 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.45→26.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 12 550 4570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.024213
X-RAY DIFFRACTIONr_bond_other_d0.0020.022823
X-RAY DIFFRACTIONr_angle_refined_deg2.0311.9535754
X-RAY DIFFRACTIONr_angle_other_deg3.95936879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92524.286196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8715653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4631521
X-RAY DIFFRACTIONr_chiral_restr0.1320.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214720
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02894
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr7.33337036
X-RAY DIFFRACTIONr_sphericity_free46.755595
X-RAY DIFFRACTIONr_sphericity_bonded15.82957375
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 396 -
Rwork0.2 7531 -
obs--97.5 %

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