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- PDB-2fm6: Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (native form) -

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Basic information

Entry
Database: PDB / ID: 2fm6
TitleZinc-beta-lactamase L1 from stenotrophomonas maltophilia (native form)
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / ZN / METALLO / LACTAMASE
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
Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 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_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_asym_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_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_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)58,56915
Polymers57,4812
Non-polymers1,08813
Water9,746541
1
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,50510
Polymers28,7401
Non-polymers7659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0635
Polymers28,7401
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,01020
Polymers57,4812
Non-polymers1,52918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area3170 Å2
ΔGint-278 kcal/mol
Surface area23560 Å2
MethodPISA
4
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,01020
Polymers57,4812
Non-polymers1,52918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area4410 Å2
ΔGint-237 kcal/mol
Surface area22210 Å2
MethodPISA
5
B: Metallo-beta-lactamase L1
hetero molecules

B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,12710
Polymers57,4812
Non-polymers6468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area4430 Å2
ΔGint-239 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.070, 105.070, 196.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-403-

ZN

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979667 / Wavelength: 0.979667 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979667 Å / Relative weight: 1
ReflectionResolution: 1.75→45.5 Å / Num. all: 60974 / Num. obs: 64243 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.8
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2 / Rsym value: 0.403 / % possible all: 99.5

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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: 1.75→45.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.067 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20301 3256 5.1 %RANDOM
Rwork0.17616 ---
all0.1775 60974 --
obs0.1775 60974 99.5 %-
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: 17.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 47 541 4590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214132
X-RAY DIFFRACTIONr_bond_other_d0.0020.023710
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9555618
X-RAY DIFFRACTIONr_angle_other_deg0.82338602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.565516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024580
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02808
X-RAY DIFFRACTIONr_nbd_refined0.3480.2925
X-RAY DIFFRACTIONr_nbd_other0.2560.24351
X-RAY DIFFRACTIONr_nbtor_other0.0830.22321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2400
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.247
X-RAY DIFFRACTIONr_mcbond_it0.7791.52634
X-RAY DIFFRACTIONr_mcangle_it1.40224177
X-RAY DIFFRACTIONr_scbond_it2.23131498
X-RAY DIFFRACTIONr_scangle_it3.5974.51441
LS refinement shellResolution: 1.753→1.799 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 233
Rwork0.219 4322

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