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- PDB-6u13: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 6u13
TitleCrystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed antibiotic moxalactam
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / lactam antibiotics / moxalactam / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
Chem-MX1 / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed antibiotic moxalactam.
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9127
Polymers29,1731
Non-polymers7396
Water5,242291
1
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,64928
Polymers116,6914
Non-polymers2,95724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area14870 Å2
ΔGint-357 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.918, 103.918, 98.929
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-666-

HOH

31A-673-

HOH

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Components

#1: Protein Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)


Mass: 29172.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt2667 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical ChemComp-MX1 / (2R)-2-((R)-CARBOXY{[CARBOXY(4-HYDROXYPHENYL)ACETYL]AMINO}METHOXYMETHYL)-5-METHYLENE-5,6-DIHYDRO-2H-1,3-OXAZINE-4-CARBO XYLIC ACID / MOXALACTAM (HYDROLYZED)


Mass: 422.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M citrate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 48271 / % possible obs: 98.4 % / Redundancy: 17.3 % / Biso Wilson estimate: 13.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 33.4
Reflection shellResolution: 1.52→1.55 Å / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 1818 / CC1/2: 0.631 / % possible all: 75.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6U0Y

6u0y


Resolution: 1.52→35.83 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.4938 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.1604 2477 5.14 %random
Rwork0.1275 45750 --
obs0.1292 48227 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.13 Å2
Refinement stepCycle: LAST / Resolution: 1.52→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 0 291 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492166
X-RAY DIFFRACTIONf_angle_d0.81662962
X-RAY DIFFRACTIONf_chiral_restr0.0512324
X-RAY DIFFRACTIONf_plane_restr0.0054396
X-RAY DIFFRACTIONf_dihedral_angle_d13.24751290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.550.27481240.23332261X-RAY DIFFRACTION89.83
1.55-1.580.27241280.18692395X-RAY DIFFRACTION95.53
1.58-1.620.18811580.15232464X-RAY DIFFRACTION98.76
1.62-1.660.20261240.13672546X-RAY DIFFRACTION100
1.66-1.70.18081570.11692499X-RAY DIFFRACTION100
1.7-1.740.16741400.10872529X-RAY DIFFRACTION100
1.74-1.790.16581180.10232555X-RAY DIFFRACTION100
1.79-1.850.15491400.10752503X-RAY DIFFRACTION99.92
1.85-1.920.15261410.10372551X-RAY DIFFRACTION100
1.92-20.15581280.10412564X-RAY DIFFRACTION100
2-2.090.16371150.1052552X-RAY DIFFRACTION100
2.09-2.20.11881340.10952561X-RAY DIFFRACTION100
2.2-2.330.15381500.11332545X-RAY DIFFRACTION100
2.33-2.510.1571390.12282569X-RAY DIFFRACTION100
2.51-2.770.15371350.12842596X-RAY DIFFRACTION100
2.77-3.170.16521450.13792606X-RAY DIFFRACTION100
3.17-3.990.15731560.13112647X-RAY DIFFRACTION100
3.99-35.830.14261450.14272807X-RAY DIFFRACTION99.97

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