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- PDB-5xe5: Discovery and structural analysis of a phloretin hydrolase from t... -

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Basic information

Entry
Database: PDB / ID: 5xe5
TitleDiscovery and structural analysis of a phloretin hydrolase from the opportunistic pathogen Mycobacterium abscessus
Componentsphloretin hydrolase
KeywordsHYDROLASE / phloretin hydrolase / Bet v1 fold / C-C bond / flavonoid
Function / homologyphloretin hydrolase / phloretin hydrolase activity / DAPG hydrolase, PhiG domain / DAPG hydrolase PhiG domain / metal ion binding / Phloretin hydrolase
Function and homology information
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHe, Y.X. / Han, J.T. / Jia, W.J. / Zhang, Z.
CitationJournal: FEBS J. / Year: 2019
Title: Discovery and structural analysis of a phloretin hydrolase from the opportunistic human pathogen Mycobacterium abscessus.
Authors: Han, J.T. / Zhang, S.P. / Jia, W.J. / Zhang, Z. / Wang, Y. / He, Y.X.
History
DepositionApr 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phloretin hydrolase
B: phloretin hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0486
Polymers63,8752
Non-polymers1734
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-6 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.185, 63.118, 74.916
Angle α, β, γ (deg.)90.000, 103.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein phloretin hydrolase


Mass: 31937.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: MAB_4487c / Production host: Escherichia coli (E. coli) / References: UniProt: B1MK49
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Na-cacodylate pH 5.0, 1 M LiCl, 6.8% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 34081 / % possible obs: 97.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.086 / Χ2: 0.851 / Net I/av σ(I): 12.737 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.17-2.212.70.3510.814183.1
2.21-2.253.20.2890.779194.9
2.25-2.293.30.2910.837196.2
2.29-2.343.30.2650.853197.5
2.34-2.393.30.2490.859198.9
2.39-2.443.40.2490.857198.3
2.44-2.513.30.2170.867199.7
2.51-2.573.20.1930.928197.8
2.57-2.653.50.1690.869198.8
2.65-2.733.50.1570.861199.1
2.73-2.833.50.1310.898198.8
2.83-2.953.40.1180.86199
2.95-3.083.30.1040.971198.8
3.08-3.243.20.0870.98198.6
3.24-3.443.50.0710.876198.7
3.44-3.713.40.0640.897198.9
3.71-4.083.30.0540.839199.3
4.08-4.673.40.0470.729199
4.67-5.893.30.0490.711199.6
5.89-503.30.0480.723199.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HWP

3hwp


Resolution: 2.17→36.786 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.45
RfactorNum. reflection% reflection
Rfree0.249 1587 5.07 %
Rwork0.2011 --
obs0.2037 31316 89.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.72 Å2 / Biso mean: 35.6812 Å2 / Biso min: 13.16 Å2
Refinement stepCycle: LAST / Resolution: 2.17→36.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 10 91 4623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084688
X-RAY DIFFRACTIONf_angle_d1.1386408
X-RAY DIFFRACTIONf_chiral_restr0.046652
X-RAY DIFFRACTIONf_plane_restr0.006848
X-RAY DIFFRACTIONf_dihedral_angle_d13.5271662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.158-2.22760.3406760.23311670174655
2.2276-2.30720.27151260.23882091221771
2.3072-2.39960.33131050.23632425253080
2.3996-2.50880.30331340.24152712284689
2.5088-2.6410.30861690.24572838300795
2.641-2.80640.3041540.25632957311199
2.8064-3.0230.33341510.25242992314399
3.023-3.3270.2951420.22842993313599
3.327-3.8080.24621680.20112997316599
3.808-4.79610.19411730.15143009318299
4.7961-36.79120.18331890.15193045323499

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