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- PDB-2fu6: Zinc-beta-lactamase l1 from stenotrophomonas maltophilia (apo form) -

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Basic information

Entry
Database: PDB / ID: 2fu6
TitleZinc-beta-lactamase l1 from stenotrophomonas maltophilia (apo form)
ComponentsMetallo-beta-lactamase L1
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
Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNauton, L. / Garau, G. / Kahn, R. / Dideberg, O.
Citation
Journal: To be Published
Title: Crystal structure of the zinc-beta-lactamase L1 from stenotrophomonas maltophilia (apo form)
Authors: Nauton, L. / Garau, G. / Kahn, R. / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)58,52613
Polymers57,4812
Non-polymers1,04511
Water9,476526
1
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3097
Polymers28,7401
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2176
Polymers28,7401
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Metallo-beta-lactamase L1
B: Metallo-beta-lactamase L1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)117,05126
Polymers114,9624
Non-polymers2,09022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area13620 Å2
ΔGint-182 kcal/mol
Surface area39550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.050, 105.050, 196.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#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 / Cellular location: PERIPLASM / 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
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: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541791
21.54181
ReflectionResolution: 2.05→20 Å / Num. obs: 40479 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 7.4
Reflection shellResolution: 2.05→2.103 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.49 / % possible all: 99.1

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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: 2.05→19.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.745 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20937 2023 5 %RANDOM
Rwork0.16038 ---
all0.1631 ---
obs0.16286 38425 98.9 %-
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: 18.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 58 526 4586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214173
X-RAY DIFFRACTIONr_bond_other_d0.0040.023769
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9665677
X-RAY DIFFRACTIONr_angle_other_deg0.86638719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82323.258178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77315616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5671532
X-RAY DIFFRACTIONr_chiral_restr0.0960.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024617
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02817
X-RAY DIFFRACTIONr_nbd_refined0.3410.2904
X-RAY DIFFRACTIONr_nbd_other0.2010.23716
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21965
X-RAY DIFFRACTIONr_nbtor_other0.0870.22281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2051.53359
X-RAY DIFFRACTIONr_mcbond_other0.2331.51085
X-RAY DIFFRACTIONr_mcangle_it1.40224203
X-RAY DIFFRACTIONr_scbond_it2.47331746
X-RAY DIFFRACTIONr_scangle_it3.4944.51471
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 147 -
Rwork0.196 2734 -
obs--97.63 %

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