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- PDB-5dpx: 1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc me... -

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Basic information

Entry
Database: PDB / ID: 5dpx
Title1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases.
ComponentsMetallo-beta-lactamase L1 type 3
KeywordsHYDROLASE / METALLO / ZN / LACTAMASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNauton, L. / Garau, G. / Khan, R. / Dideberg, O.
Citation
Journal: ChemMedChem / Year: 2017
Title: 1,2,4-Triazole-3-thione Compounds as Inhibitors of Dizinc Metallo-beta-lactamases.
Authors: Sevaille, L. / Gavara, L. / Bebrone, C. / De Luca, F. / Nauton, L. / Achard, M. / Mercuri, P. / Tanfoni, S. / Borgianni, L. / Guyon, C. / Lonjon, P. / Turan-Zitouni, G. / Dzieciolowski, J. / ...Authors: Sevaille, L. / Gavara, L. / Bebrone, C. / De Luca, F. / Nauton, L. / Achard, M. / Mercuri, P. / Tanfoni, S. / Borgianni, L. / Guyon, C. / Lonjon, P. / Turan-Zitouni, G. / Dzieciolowski, J. / Becker, K. / Benard, L. / Condon, C. / Maillard, L. / Martinez, J. / Frere, J.M. / Dideberg, O. / Galleni, M. / Docquier, J.D. / Hernandez, J.F.
#1: Journal: Antimicrob.Agents Chemother. / Year: 2004
Title: Update Of The Standard Numbering Scheme For Class B Beta-Lactamases
Authors: Garau, G. / Garcia-Saez, I. / Bebrone, C. / Anne, C. / Mercuri, P. / Galleni, M. / Frere, J.-M. / Dideberg, O.
#2: Journal: Embo J. / Year: 1995
Title: The 3-D Structure Of A Zinc Metallo-Beta-Lactamase From Bacillus Cereus Reveals A New Type Of Protein Fold
Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.-M. / Dideberg, O.
#3: Journal: J.Mol.Biol. / Year: 2008
Title: Structural Insights Into The Design Of Inhibitors For The L1 Metallo-Beta-Lactamase From Stenotrophomonas Maltophilia.
Authors: Nauton, L. / Kahn, R. / Garau, G. / Hernandez, J.F. / Dideberg, O.
History
DepositionSep 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.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

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase L1 type 3
B: Metallo-beta-lactamase L1 type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,50512
Polymers57,4812
Non-polymers1,02410
Water9,332518
1
A: Metallo-beta-lactamase L1 type 3
B: Metallo-beta-lactamase L1 type 3
hetero molecules

A: Metallo-beta-lactamase L1 type 3
B: Metallo-beta-lactamase L1 type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,01124
Polymers114,9624
Non-polymers2,04920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area10850 Å2
ΔGint-124 kcal/mol
Surface area40100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.040, 105.040, 196.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-728-

HOH

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Components

#1: Protein Metallo-beta-lactamase L1 type 3 / B3 metallo-beta-lactamase / Beta-lactamase type III / Metallo-beta-lactamase L1 type III / Penicillinase


Mass: 28740.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Cellular location: PERIPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P52700, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-L3B / 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione


Mass: 189.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7N3S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 1.8M AMMONIUM SULFATE, 0.1M HEPES, PH7.75, 1.5% V/V PEG 400, VAPOR DIFFUSION, HANGING DROP.
PH range: 7.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2006 / Details: Xenocs multilayers mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→19.85 Å / Num. obs: 53574 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 12.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.385 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2057: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HB9

2hb9


Resolution: 1.85→19.851 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 2000 3.73 %Random selection
Rwork0.167 ---
obs0.1684 53574 96.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→19.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4004 0 50 518 4572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064220
X-RAY DIFFRACTIONf_angle_d0.9815775
X-RAY DIFFRACTIONf_dihedral_angle_d11.2092473
X-RAY DIFFRACTIONf_chiral_restr0.045630
X-RAY DIFFRACTIONf_plane_restr0.005762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.2641370.21683525X-RAY DIFFRACTION94
1.8963-1.94750.22541370.19893559X-RAY DIFFRACTION95
1.9475-2.00470.23611380.18623527X-RAY DIFFRACTION95
2.0047-2.06940.24021390.17483601X-RAY DIFFRACTION95
2.0694-2.14330.20831400.16273597X-RAY DIFFRACTION96
2.1433-2.2290.20921390.15043601X-RAY DIFFRACTION96
2.229-2.33030.18561410.15033654X-RAY DIFFRACTION96
2.3303-2.45290.21171420.15613645X-RAY DIFFRACTION97
2.4529-2.60630.20741420.16443678X-RAY DIFFRACTION97
2.6063-2.8070.23261450.17113709X-RAY DIFFRACTION98
2.807-3.08850.20951460.16693771X-RAY DIFFRACTION98
3.0885-3.53330.19341470.16153776X-RAY DIFFRACTION98
3.5333-4.44330.18371490.15023870X-RAY DIFFRACTION99
4.4433-19.85180.18821580.17774061X-RAY DIFFRACTION98

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