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- PDB-5xr3: SAV0551 with glyoxylate -

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Basic information

Entry
Database: PDB / ID: 5xr3
TitleSAV0551 with glyoxylate
ComponentsProtein/nucleic acid deglycase HchA
KeywordsCHAPERONE / Hsp31 / glyoxalase III
Function / homology
Function and homology information


thiolester hydrolase activity / protein repair / protein deglycase / protein deglycase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on ester bonds; Thioester hydrolases / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / DNA repair / cytoplasm
Similarity search - Function
Protein/nucleic acid deglycase HchA / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYOXYLIC ACID / Protein/nucleic acid deglycase HchA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsKim, H.J. / Kwon, A.R. / Lee, B.J.
CitationJournal: Biosci. Rep. / Year: 2017
Title: Structural and functional studies of SAV0551 fromStaphylococcus aureusas a chaperone and glyoxalase III.
Authors: Kim, H.J. / Lee, K.Y. / Kwon, A.R. / Lee, B.J.
History
DepositionJun 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Protein/nucleic acid deglycase HchA
B: Protein/nucleic acid deglycase HchA
C: Protein/nucleic acid deglycase HchA
D: Protein/nucleic acid deglycase HchA
E: Protein/nucleic acid deglycase HchA
F: Protein/nucleic acid deglycase HchA
G: Protein/nucleic acid deglycase HchA
H: Protein/nucleic acid deglycase HchA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,01010
Polymers266,8628
Non-polymers1482
Water1267
1
A: Protein/nucleic acid deglycase HchA
B: Protein/nucleic acid deglycase HchA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7903
Polymers66,7162
Non-polymers741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-6 kcal/mol
Surface area22790 Å2
MethodPISA
2
C: Protein/nucleic acid deglycase HchA
D: Protein/nucleic acid deglycase HchA


Theoretical massNumber of molelcules
Total (without water)66,7162
Polymers66,7162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-8 kcal/mol
Surface area22850 Å2
MethodPISA
3
E: Protein/nucleic acid deglycase HchA
F: Protein/nucleic acid deglycase HchA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7903
Polymers66,7162
Non-polymers741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-5 kcal/mol
Surface area22290 Å2
MethodPISA
4
G: Protein/nucleic acid deglycase HchA
H: Protein/nucleic acid deglycase HchA


Theoretical massNumber of molelcules
Total (without water)66,7162
Polymers66,7162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-8 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.199, 130.125, 187.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein/nucleic acid deglycase HchA / Maillard deglycase / Protein deglycase HchA


Mass: 33357.773 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: hchA, SAV0551 / Production host: Escherichia coli (E. coli)
References: UniProt: P64312, Hydrolases; Acting on ester bonds; Thioester hydrolases, protein deglycase
#2: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 30% (w/v) PEG 3350, 100mM BisTris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→50 Å / Num. obs: 47559 / % possible obs: 99.8 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.216 / Rsym value: 0.207 / Net I/σ(I): 20.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XR2

5xr2


Resolution: 3.01→50.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.873 / SU B: 21.005 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2428 5.1 %RANDOM
Rwork0.181 ---
obs0.185 45071 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.01→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17825 0 10 7 17842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01918196
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217088
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.99224663
X-RAY DIFFRACTIONr_angle_other_deg0.991339920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93552271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.56925.925773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.416153185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5451548
X-RAY DIFFRACTIONr_chiral_restr0.0770.22780
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120017
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023241
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_it2.4424.6239156
X-RAY DIFFRACTIONr_mcbond_other2.444.6239155
X-RAY DIFFRACTIONr_mcangle_it3.9576.92611403
X-RAY DIFFRACTIONr_mcangle_other3.9576.92611404
X-RAY DIFFRACTIONr_scbond_it2.6494.9399040
X-RAY DIFFRACTIONr_scbond_other2.6494.9399041
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4557.2813261
X-RAY DIFFRACTIONr_long_range_B_refined6.89153.7819121
X-RAY DIFFRACTIONr_long_range_B_other6.89153.78419122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.01→3.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 159 -
Rwork0.238 3003 -
obs--90.97 %

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