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- PDB-4ysl: Crystal structure of SdoA from Pseudomonas putida in complex with... -

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Basic information

Entry
Database: PDB / ID: 4ysl
TitleCrystal structure of SdoA from Pseudomonas putida in complex with glutathione
ComponentsBeta-lactamase domain protein
KeywordsHYDROLASE / Sulfur dioxygenase / ETHE1 / glutathione
Function / homology
Function and homology information


sulfur dioxygenase activity / glutathione metabolic process / metal ion binding
Similarity search - Function
Persulfide dioxygenase-like, MBL-fold metallo-hydrolase domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / GLUTATHIONE / Beta-lactamase domain protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4618 Å
AuthorsSattler, S.A. / Wang, X. / DeHan, P.J. / Xun, L. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Characterizations of Two Bacterial Persulfide Dioxygenases of the Metallo-beta-lactamase Superfamily.
Authors: Sattler, S.A. / Wang, X. / Lewis, K.M. / DeHan, P.J. / Park, C.M. / Xin, Y. / Liu, H. / Xian, M. / Xun, L. / Kang, C.
History
DepositionMar 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_auth_seq_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: Beta-lactamase domain protein
B: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0866
Polymers65,3602
Non-polymers7264
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-55 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.625, 79.625, 93.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Beta-lactamase domain protein


Mass: 32680.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain F1 / ATCC 700007) (bacteria)
Strain: F1 / ATCC 700007 / Gene: Pput_0068 / Production host: Escherichia coli (E. coli) / References: UniProt: A5VWI3
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200 mM Ammonium acetate, 100 mM HEPES (pH 7.5), and 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. all: 101163 / Num. obs: 100527 / % possible obs: 98.18 % / Redundancy: 2.4 % / Net I/σ(I): 30.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementResolution: 1.4618→40.459 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 1971 1.99 %
Rwork0.1765 --
obs0.177 99194 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4618→40.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 42 694 5318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144962
X-RAY DIFFRACTIONf_angle_d1.5466755
X-RAY DIFFRACTIONf_dihedral_angle_d13.6681851
X-RAY DIFFRACTIONf_chiral_restr0.102738
X-RAY DIFFRACTIONf_plane_restr0.009916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4618-1.49830.34231290.30596321X-RAY DIFFRACTION89
1.4983-1.53880.32511380.27286676X-RAY DIFFRACTION95
1.5388-1.58410.30541370.24916865X-RAY DIFFRACTION97
1.5841-1.63520.23851390.22986903X-RAY DIFFRACTION98
1.6352-1.69370.22441430.22066939X-RAY DIFFRACTION99
1.6937-1.76150.28551440.20866979X-RAY DIFFRACTION99
1.7615-1.84170.21711450.20247034X-RAY DIFFRACTION100
1.8417-1.93880.2781390.20167060X-RAY DIFFRACTION100
1.9388-2.06020.19461460.18576980X-RAY DIFFRACTION100
2.0602-2.21930.2171390.17217071X-RAY DIFFRACTION100
2.2193-2.44260.21971390.17687071X-RAY DIFFRACTION100
2.4426-2.7960.18391470.17757068X-RAY DIFFRACTION100
2.796-3.52230.17911410.1697100X-RAY DIFFRACTION100
3.5223-40.47410.17281450.14287156X-RAY DIFFRACTION99

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