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- PDB-6cky: Crystal structure of UcmS2 -

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Basic information

Entry
Database: PDB / ID: 6cky
TitleCrystal structure of UcmS2
ComponentsGlyoxalase
KeywordsANTITOXIN / resistance
Function / homology
Function and homology information


lactoylglutathione lyase activity / dioxygenase activity / metal ion binding
Similarity search - Function
Glyoxalase I, conserved site / Glyoxalase I signature 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
Similarity search - Domain/homology
Biological speciesStreptomyces uncialis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChang, C.Y. / Chang, C. / Annaval, T. / Babnigg, G. / Phillips Jr., G.N. / Joachimiak, A. / Shen, B.
CitationJournal: To Be Published
Title: Crystal structure of UcmS2
Authors: Chang, C.Y. / Chang, C. / Annaval, T. / Babnigg, G. / Phillips Jr., G.N. / Joachimiak, A. / Shen, B.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Glyoxalase
B: Glyoxalase


Theoretical massNumber of molelcules
Total (without water)34,9992
Polymers34,9992
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-21 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.531, 75.945, 142.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

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Components

#1: Protein Glyoxalase / Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 17499.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces uncialis (bacteria) / Gene: ucmS2, AB852_17870
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A140E9J7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS, pH 5.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.8→71.46 Å / Num. obs: 24648 / % possible obs: 99.1 % / Redundancy: 8.2 % / Net I/σ(I): 42
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1101 / CC1/2: 0.897 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UMW

5umw


Resolution: 1.8→71.46 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.544 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 1167 5.1 %RANDOM
Rwork0.21106 ---
obs0.21363 21653 91.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.8→71.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 0 78 2221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192189
X-RAY DIFFRACTIONr_bond_other_d0.0020.022078
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.9512963
X-RAY DIFFRACTIONr_angle_other_deg1.09534771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53423.153111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77115371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.381523
X-RAY DIFFRACTIONr_chiral_restr0.1210.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212465
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02514
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_it2.3262.0991070
X-RAY DIFFRACTIONr_mcbond_other2.3182.0981069
X-RAY DIFFRACTIONr_mcangle_it3.5143.1311334
X-RAY DIFFRACTIONr_mcangle_other3.5153.1321335
X-RAY DIFFRACTIONr_scbond_it3.1012.5991119
X-RAY DIFFRACTIONr_scbond_other3.12.5991119
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.93.7171630
X-RAY DIFFRACTIONr_long_range_B_refined6.66624.6732339
X-RAY DIFFRACTIONr_long_range_B_other6.66224.6192329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 40 -
Rwork0.232 708 -
obs--41.58 %

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