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- PDB-5xr2: SAV0551 -

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Basic information

Entry
Database: PDB / ID: 5xr2
TitleSAV0551
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
LACTIC ACID / Protein/nucleic acid deglycase HchA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 7, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)266,51511
Polymers266,2708
Non-polymers2463
Water5,044280
1
A: Protein/nucleic acid deglycase HchA
B: Protein/nucleic acid deglycase HchA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6583
Polymers66,5672
Non-polymers901
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-8 kcal/mol
Surface area22880 Å2
MethodPISA
2
C: Protein/nucleic acid deglycase HchA
D: Protein/nucleic acid deglycase HchA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6333
Polymers66,5672
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-7 kcal/mol
Surface area23190 Å2
MethodPISA
3
E: Protein/nucleic acid deglycase HchA
F: Protein/nucleic acid deglycase HchA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6583
Polymers66,5672
Non-polymers901
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-7 kcal/mol
Surface area22420 Å2
MethodPISA
4
G: Protein/nucleic acid deglycase HchA
H: Protein/nucleic acid deglycase HchA


Theoretical massNumber of molelcules
Total (without water)66,5672
Polymers66,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-29 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.284, 129.454, 187.853
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: 33283.738 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-LAC / LACTIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 23% (w/v) PEG 3350, 100mM BisTris, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 72192 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.044 / Rsym value: 0.107 / Net I/σ(I): 32.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.475 / Num. unique obs: 3475 / CC1/2: 0.837 / Rpim(I) all: 0.186 / Rsym value: 0.437 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data processing
HKL-2000data scaling
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4N

4i4n


Resolution: 2.6→48.65 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.742 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25423 3580 5 %RANDOM
Rwork0.18093 ---
obs0.18459 68531 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.6→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17891 0 13 280 18184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01918289
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217109
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.98524817
X-RAY DIFFRACTIONr_angle_other_deg1.011339984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13452298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40225.873785
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.233153202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1471548
X-RAY DIFFRACTIONr_chiral_restr0.0860.22785
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120210
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023274
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_it2.6253.9529216
X-RAY DIFFRACTIONr_mcbond_other2.6243.9529215
X-RAY DIFFRACTIONr_mcangle_it4.075.92111506
X-RAY DIFFRACTIONr_mcangle_other4.0715.92111507
X-RAY DIFFRACTIONr_scbond_it3.0014.3149073
X-RAY DIFFRACTIONr_scbond_other34.3149074
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8356.31713312
X-RAY DIFFRACTIONr_long_range_B_refined6.60246.09319403
X-RAY DIFFRACTIONr_long_range_B_other6.646.09619378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 232 -
Rwork0.22 4667 -
obs--92.43 %

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