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- PDB-2fu8: Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (d-capto... -

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Basic information

Entry
Database: PDB / ID: 2fu8
TitleZinc-beta-lactamase L1 from stenotrophomonas maltophilia (d-captopril complex)
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / ZN / METALLO / LACTAMASE / INHIBITOR
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
Chem-MCO / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNauton, L. / Garau, G. / Kahn, R. / Dideberg, O.
Citation
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.
#1: 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.
#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
DepositionJan 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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_special_symmetry / struct_conn / struct_site
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,03817
Polymers57,4812
Non-polymers1,55715
Water12,358686
1
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,66110
Polymers28,7401
Non-polymers9219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3777
Polymers28,7401
Non-polymers6366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Metallo-beta-lactamase L1
hetero molecules

B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,03817
Polymers57,4812
Non-polymers1,55715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/31
Buried area4590 Å2
ΔGint-248 kcal/mol
Surface area23110 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-243 kcal/mol
Surface area22430 Å2
MethodPISA
5
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,32220
Polymers57,4812
Non-polymers1,84118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area4090 Å2
ΔGint-243 kcal/mol
Surface area23880 Å2
MethodPISA
6
B: Metallo-beta-lactamase L1
hetero molecules

B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,75314
Polymers57,4812
Non-polymers1,27312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area3430 Å2
ΔGint-243 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.011, 105.011, 196.615
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-2723-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 28740.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: IID 1275 / Gene: L1 / Plasmid details: PUB 5832 / Plasmid: PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P52700, beta-lactamase

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Non-polymers , 5 types, 701 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15NO3S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS COORDINATES ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE ...THIS COORDINATES ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY.

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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: 7.5
Details: AS, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.8→21.24 Å / Num. obs: 56045 / % possible obs: 90.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 5.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.416 / % possible all: 90.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SML

1sml


Resolution: 1.8→21.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.1 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.116 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18252 2717 5 %RANDOM
Rwork0.1598 ---
obs0.16093 51428 90.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.17 Å20 Å2
2--0.33 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 78 686 4766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214163
X-RAY DIFFRACTIONr_bond_other_d0.0090.023743
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9645665
X-RAY DIFFRACTIONr_angle_other_deg0.81538679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7165516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024598
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02806
X-RAY DIFFRACTIONr_nbd_refined0.3440.2933
X-RAY DIFFRACTIONr_nbd_other0.2590.24418
X-RAY DIFFRACTIONr_nbtor_other0.0830.22274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2489
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.247
X-RAY DIFFRACTIONr_mcbond_it0.7971.52642
X-RAY DIFFRACTIONr_mcangle_it1.45424194
X-RAY DIFFRACTIONr_scbond_it2.30931521
X-RAY DIFFRACTIONr_scangle_it3.7464.51471
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 209
Rwork0.297 4081

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