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- PDB-4mym: Crystal structure of a glyoxalase/ bleomycin resistance protein/ ... -

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Basic information

Entry
Database: PDB / ID: 4mym
TitleCrystal structure of a glyoxalase/ bleomycin resistance protein/ dioxygenase from Nocardioides
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsOXIDOREDUCTASE / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / metalloproteins / antibiotic resistance proteins
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 speciesNocardioides sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsEswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / AL Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a glyoxalase/ bleomycin resistance protein/ dioxygenase from Nocardioides.
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,9802
Polymers19,7701
Non-polymers2091
Water93752
1
A: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

A: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9594
Polymers39,5412
Non-polymers4182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5450 Å2
ΔGint-38 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.660, 83.589, 102.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 19770.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardioides sp. (bacteria) / Strain: BAA-499 / JS614 / Gene: Noca_4190 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A1SPF2
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1M Bis-Tris, 0.2M NaCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 14825 / Num. obs: 14825 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 20.012 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.455 / Num. unique all: 1228 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.207 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21722 746 5.1 %RANDOM
Rwork0.18641 ---
all0.218 14762 --
obs0.18798 14016 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.849 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0 Å2
2---2.15 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 14 52 1249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021232
X-RAY DIFFRACTIONr_bond_other_d0.0010.021118
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9831682
X-RAY DIFFRACTIONr_angle_other_deg0.73732583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12223.14854
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44715169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.901158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
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_it1.3242.48603
X-RAY DIFFRACTIONr_mcbond_other1.3082.473602
X-RAY DIFFRACTIONr_mcangle_it2.1753.703752
X-RAY DIFFRACTIONr_mcangle_other2.1793.709753
X-RAY DIFFRACTIONr_scbond_it1.8822.652628
X-RAY DIFFRACTIONr_scbond_other1.8812.652628
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9853.893931
X-RAY DIFFRACTIONr_long_range_B_refined4.41120.0391379
X-RAY DIFFRACTIONr_long_range_B_other4.40519.9711367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 55 -
Rwork0.314 993 -
obs-1048 96.95 %

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