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- PDB-2qdt: Structural Basis for the Broad-Spectrum Inhibition of Metallo-{Be... -

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Basic information

Entry
Database: PDB / ID: 2qdt
TitleStructural Basis for the Broad-Spectrum Inhibition of Metallo-{Beta}-Lactamases: L1- IS38 Complex
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / ZN / METALLO / LACTAMASE / INHIBITOR / L1
Function / homology
Function and homology information


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 superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(3-MERCAPTOPROPANOYL)-D-ALANINE / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarau, G. / Dideberg, O.
Citation
Journal: Org.Biomol.Chem. / Year: 2008
Title: Structural basis for the broad-spectrum inhibition of metallo-beta-lactamases by thiols.
Authors: Lienard, B.M. / Garau, G. / Horsfall, L. / Karsisiotis, A.I. / Damblon, C. / Lassaux, P. / Papamicael, C. / Roberts, G.C. / Galleni, M. / Dideberg, O. / Frere, J.M. / Schofield, C.J.
#1: Journal: Antimicrob.Agents Chemother. / Year: 2007
Title: Competitive Inhibitors of the Cpha Metallo-{Beta}-Lactamase from Aeromonas Hydrophila
Authors: Horsfall, L.E. / Garau, G. / Lienard, B.M.R. / Dideberg, O. / Schofield, C.J. / Frere, J.M. / Galleni, M.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: A Metallo-Beta-Lactamase Enzyme in Action: Crystal Structures of the Monozinc Carbapenemase Cpha and its Complex with Biapenem
Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O.
History
DepositionJun 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4028
Polymers28,7401
Non-polymers6627
Water4,179232
1
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,80416
Polymers57,4812
Non-polymers1,32314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area3550 Å2
ΔGint-351 kcal/mol
Surface area23500 Å2
MethodPISA
2
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,80416
Polymers57,4812
Non-polymers1,32314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)105.319, 105.319, 97.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-794-

HOH

21A-829-

HOH

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Components

#1: Protein Metallo-beta-lactamase L1 / Beta-lactamase type II / Penicillinase


Mass: 28740.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: IID 1275 / Gene: L1 / Plasmid: PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P52700, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-I38 / N-(3-MERCAPTOPROPANOYL)-D-ALANINE


Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG, AS, PH 6.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100K, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 22311 / Num. obs: 21311 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 28.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 11 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.404 / % possible all: 94.2

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Processing

Software
NameVersionClassification
CCP4model building
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SML

1sml


Resolution: 2→26.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.23 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.159 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19249 1092 5.1 %RANDOM
Rwork0.16988 ---
obs0.17106 20217 95.94 %-
all-22311 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.524 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2→26.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 29 232 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212087
X-RAY DIFFRACTIONr_bond_other_d0.0010.021370
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9622849
X-RAY DIFFRACTIONr_angle_other_deg0.9293.0013332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24723.14689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42515307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.731516
X-RAY DIFFRACTIONr_chiral_restr0.080.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_nbd_refined0.2030.2444
X-RAY DIFFRACTIONr_nbd_other0.1950.21474
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2985
X-RAY DIFFRACTIONr_nbtor_other0.0870.21076
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2174
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0690.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.226
X-RAY DIFFRACTIONr_mcbond_it1.0351.51692
X-RAY DIFFRACTIONr_mcbond_other0.1651.5537
X-RAY DIFFRACTIONr_mcangle_it1.1722112
X-RAY DIFFRACTIONr_scbond_it1.8753873
X-RAY DIFFRACTIONr_scangle_it2.8054.5737
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 76 -
Rwork0.205 1417 -
obs--93.08 %

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