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- PDB-2qin: Stenotrophomonas maltophilia L1 Metallo-beta-Lactamase Asp-120 Cy... -

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Basic information

Entry
Database: PDB / ID: 2qin
TitleStenotrophomonas maltophilia L1 Metallo-beta-Lactamase Asp-120 Cys mutant
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / METALLO-BETA-LACTAMASE / BINUCLEAR / DINUCLEAR
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 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: 1.76 Å
AuthorsSpencer, J.
Citation
Journal: Biochemistry / Year: 2007
Title: Structural Basis for the Role of Asp-120 in Metallo-beta-lactamases.
Authors: Crisp, J. / Conners, R. / Garrity, J.D. / Carenbauer, A.L. / Crowder, M.W. / Spencer, J.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Metal Binding Asp-120 in Metallo-beta-lactamase L1 from Stenotrophomonas maltophilia Plays a Crucial Role in Catalysis
Authors: Garrity, J.D. / Carenbauer, A.L. / Herron, L.R. / Crowder, M.W.
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 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
B: Metallo-beta-lactamase L1
C: Metallo-beta-lactamase L1
D: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,55115
Polymers114,9144
Non-polymers63711
Water23,2391290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-365 kcal/mol
Surface area38870 Å2
MethodPISA, PQS
2
A: Metallo-beta-lactamase L1
B: Metallo-beta-lactamase L1
hetero molecules

C: Metallo-beta-lactamase L1
D: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,55115
Polymers114,9144
Non-polymers63711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6890 Å2
ΔGint-397 kcal/mol
Surface area42500 Å2
MethodPISA
3
A: Metallo-beta-lactamase L1
B: Metallo-beta-lactamase L1
hetero molecules

C: Metallo-beta-lactamase L1
D: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,55115
Polymers114,9144
Non-polymers63711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area7090 Å2
ΔGint-359 kcal/mol
Surface area42200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.141, 112.845, 78.352
Angle α, β, γ (deg.)90.00, 113.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28728.508 Da / Num. of mol.: 4 / Mutation: D120C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: IID 1275 / Gene: L1 / Plasmid: pUB5832 / 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.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1290 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris.Cl, 0.2M MgCl2, 18% PEG 4000, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. all: 104385 / Num. obs: 98730 / % possible obs: 94.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 18.795 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24
Reflection shellResolution: 1.76→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 7 / Num. unique all: 13052 / % possible all: 69.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SML

1sml


Resolution: 1.76→26.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.187 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4969 5 %RANDOM
Rwork0.173 ---
obs0.175 98579 94.35 %-
all-104385 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.043 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.76→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7934 0 11 1290 9235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0218138
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.95311118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37451053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02623.195338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.341151195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.911559
X-RAY DIFFRACTIONr_chiral_restr0.0650.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026303
X-RAY DIFFRACTIONr_nbd_refined0.180.23938
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.21056
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.244
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0970.21
X-RAY DIFFRACTIONr_mcbond_it0.4151.55398
X-RAY DIFFRACTIONr_mcangle_it0.69928381
X-RAY DIFFRACTIONr_scbond_it1.06733140
X-RAY DIFFRACTIONr_scangle_it1.764.52736
LS refinement shellResolution: 1.759→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 278 -
Rwork0.23 4571 -
obs-4849 63.12 %

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