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- PDB-6u10: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 6u10
TitleCrystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the inhibitor captopril
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / metallo-beta-lactamases / lactam antibiotics / penicillin G / 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / L-CAPTOPRIL / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 inhibitor captopril.
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)29,98410
Polymers29,1731
Non-polymers8129
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)119,93840
Polymers116,6914
Non-polymers3,24636
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_445-y-1,-x-1,-z+1/31
Buried area13430 Å2
ΔGint-127 kcal/mol
Surface area39920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.537, 104.537, 98.723
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-413-

HOH

21A-422-

HOH

31A-456-

HOH

41A-655-

HOH

51A-665-

HOH

61A-684-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 300 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-X8Z / L-CAPTOPRIL / Captopril


Mass: 217.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor, medication*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


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

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Details

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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 8 % (v/v) Tacimate pH 7, 20 % (w/v) PEG3350, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 63060 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 19.84 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 26.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3071 / CC1/2: 0.525 / % possible all: 98.5

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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: 1.4→46.22 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.167 3172 -
Rwork0.145 --
obs0.146 59802 99.6 %
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 46 291 2360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052229
X-RAY DIFFRACTIONf_angle_d0.823044
X-RAY DIFFRACTIONf_chiral_restr0.074332
X-RAY DIFFRACTIONf_plane_restr0.005409
X-RAY DIFFRACTIONf_dihedral_angle_d22.96818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.24771270.24022376X-RAY DIFFRACTION0.93
1.42-1.440.27821340.22232543X-RAY DIFFRACTION0.99
1.44-1.460.22521140.19642578X-RAY DIFFRACTION1
1.46-1.490.21581340.17752583X-RAY DIFFRACTION1
1.49-1.520.20291250.16052581X-RAY DIFFRACTION1
1.52-1.550.20961530.14172560X-RAY DIFFRACTION1
1.55-1.580.18341420.13382560X-RAY DIFFRACTION1
1.58-1.610.16331390.12142565X-RAY DIFFRACTION1
1.61-1.650.14381560.1212557X-RAY DIFFRACTION1
1.65-1.690.16371410.11932588X-RAY DIFFRACTION1
1.69-1.740.16021450.1172568X-RAY DIFFRACTION1
1.74-1.790.1611350.12222587X-RAY DIFFRACTION1
1.79-1.840.17971340.12382596X-RAY DIFFRACTION1
1.84-1.910.15451330.12582605X-RAY DIFFRACTION1
1.91-1.990.14791420.12272585X-RAY DIFFRACTION1
1.99-2.080.15561380.12822601X-RAY DIFFRACTION1
2.08-2.190.15831220.13012634X-RAY DIFFRACTION1
2.19-2.320.16161520.13022618X-RAY DIFFRACTION1
2.32-2.50.14521450.14352615X-RAY DIFFRACTION1
2.5-2.760.14611190.15252682X-RAY DIFFRACTION1
2.76-3.150.17541420.16032659X-RAY DIFFRACTION1
3.15-3.970.18721410.14752704X-RAY DIFFRACTION1
3.97-46.220.161590.15382857X-RAY DIFFRACTION1

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