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- PDB-5dtt: Fragments bound to the OXA-48 beta-lactamase: Compound 3 -

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Basic information

Entry
Database: PDB / ID: 5dtt
TitleFragments bound to the OXA-48 beta-lactamase: Compound 3
ComponentsBeta-lactamase
KeywordsHYDROLASE / inhibitor / complex / fragment / lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(1,3-thiazol-2-yl)benzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10000527 Å
AuthorsLund, B.A. / Christopeit, T. / Leiros, H.-K.S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.
Authors: Lund, B.A. / Christopeit, T. / Guttormsen, Y. / Bayer, A. / Leiros, H.K.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7369
Polymers113,1924
Non-polymers5435
Water24,1401340
1
A: Beta-lactamase
hetero molecules

C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8374
Polymers56,5962
Non-polymers2412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y+1/2,-z+1/21
2
C: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8374
Polymers56,5962
Non-polymers2412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_745-x+2,y-1/2,-z+1/21
3
B: Beta-lactamase
hetero molecules

D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8995
Polymers56,5962
Non-polymers3033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_794-x+5/2,-y+4,z-1/21
4
D: Beta-lactamase
hetero molecules

B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8995
Polymers56,5962
Non-polymers3033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_795-x+5/2,-y+4,z+1/21
Unit cell
Length a, b, c (Å)88.371, 107.622, 124.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Beta-lactamase


Mass: 28298.029 Da / Num. of mol.: 4 / Fragment: UNP residues 22-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-5F5 / 3-(1,3-thiazol-2-yl)benzoic acid


Mass: 205.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7NO2S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1340 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 8-12% PEG8000, 4% 1-butanol / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→45.96 Å / Num. obs: 69611 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.2513417337 Å2 / Rmerge(I) obs: 0.1608 / Net I/σ(I): 6.35
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7949 / Mean I/σ(I) obs: 1.54 / Num. unique all: 6874 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2328refinement
XDS20141118data reduction
PHASER2.5.6phasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.10000527→45.9606680821 Å / SU ML: 0.291797265807 / Cross valid method: FREE R-VALUE / σ(F): 1.33553952209 / Phase error: 27.8656366962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.246183444911 6568 5.01381700484 %Random selection
Rwork0.200916879833 124430 --
obs0.203233976136 130998 97.8137180234 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.6309030722 Å2
Refinement stepCycle: LAST / Resolution: 2.10000527→45.9606680821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7924 0 34 1340 9298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002297496547418173
X-RAY DIFFRACTIONf_angle_d0.49531117481811064
X-RAY DIFFRACTIONf_chiral_restr0.04235153961631159
X-RAY DIFFRACTIONf_plane_restr0.001582303753861452
X-RAY DIFFRACTIONf_dihedral_angle_d18.67018189064811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.334945437472140.3189943594984174X-RAY DIFFRACTION98.606741573
2.1239-2.14890.331958081332310.3063150309614193X-RAY DIFFRACTION98.2892690513
2.1489-2.17510.3381396481592360.3056501913164125X-RAY DIFFRACTION98.5314053321
2.1751-2.20260.3393833259342220.2909494257714204X-RAY DIFFRACTION98.3118613949
2.2026-2.23160.3362284562982060.3009822322264110X-RAY DIFFRACTION97.9573309124
2.2316-2.26210.3777690113252380.2968282819764165X-RAY DIFFRACTION97.7141588992
2.2621-2.29450.3278698298021980.2836527512114149X-RAY DIFFRACTION97.7293165468
2.2945-2.32870.3382840667632080.2817310247974167X-RAY DIFFRACTION97.7653631285
2.3287-2.36510.3261073573372060.2844729719784133X-RAY DIFFRACTION97.5275342774
2.3651-2.40390.3424392670842180.268225835584076X-RAY DIFFRACTION95.8696137531
2.4039-2.44530.3164778803742280.262286875934101X-RAY DIFFRACTION96.8673081226
2.4453-2.48980.3131615243352280.2557443577384140X-RAY DIFFRACTION97.3045221653
2.4898-2.53770.2658473033532390.2459651590954091X-RAY DIFFRACTION97.963800905
2.5377-2.58950.2921177773592220.23619336324200X-RAY DIFFRACTION98.4855233853
2.5895-2.64580.2794875558582300.2399221139174119X-RAY DIFFRACTION98.1494019409
2.6458-2.70730.2972090340391790.2338778753014235X-RAY DIFFRACTION98.3730777803
2.7073-2.7750.2847150699082300.2141609702134179X-RAY DIFFRACTION98.5471613768
2.775-2.850.2474551908842290.2028588850834151X-RAY DIFFRACTION98.670871818
2.85-2.93390.2406860098422040.1977379784694194X-RAY DIFFRACTION98.1696428571
2.9339-3.02850.23044725751960.1973063005414184X-RAY DIFFRACTION98.1622590766
3.0285-3.13680.2409438334421830.1877515190854141X-RAY DIFFRACTION96.6905187835
3.1368-3.26230.2465858729352230.1983399981674094X-RAY DIFFRACTION96.8806104129
3.2623-3.41070.2085605450422060.1671925862624172X-RAY DIFFRACTION98.0295566502
3.4107-3.59050.2223416044912500.1518916444414147X-RAY DIFFRACTION98.3889013202
3.5905-3.81540.1884585933062290.136154148734149X-RAY DIFFRACTION98.2054733064
3.8154-4.10980.1533322597172480.1243153232564131X-RAY DIFFRACTION98.1838565022
4.1098-4.5230.1560004309271750.1286921863884165X-RAY DIFFRACTION97.3312401884
4.523-5.17680.1819415028892550.1414124701414077X-RAY DIFFRACTION96.3737486096
5.1768-6.51920.227501632352090.164751217564151X-RAY DIFFRACTION98.4198645598
6.5192-45.97170.2299679945182280.1751759818974113X-RAY DIFFRACTION96.9839142091
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9076706176540.222823451979-0.1012037911671.164871171390.2037067130670.812760273403-0.04806168081080.002547743830410.0245605880481-0.04572265555540.04139778353990.07748642969760.0008664490363910.0168814014790.02085933367420.2872809924870.01180776385730.05407498354720.2364513397790.01159625707140.18844763627388.7335670533259.3182841332.4821762525
20.430414337333-0.1497779823330.3482207527741.187661790830.09298024772191.220217977620.0160764078113-0.0205705446490.001448138304750.06555229565290.0163397613813-0.05337577234330.1003923103370.0921540594484-0.03870703731560.233101231758-0.001392953429760.09607108830990.187410326454-0.004225408280150.16682202206388.6480230453219.899413158-2.49066857326
30.7773093939370.1600844545210.4579124850791.50882018363-0.3681374147071.29322438334-0.01845320858060.07575963975860.0269888309959-0.03728670903140.03947113836870.03767087990320.0671087287495-0.12630099954-0.02676634824580.232446630928-0.01614531285960.1150731439670.2463927753420.007516384137620.20083675878884.6385801771222.20868311632.0679959384
40.8111015665690.3911594988390.04860188019371.35743838315-0.4504401767451.49224215646-0.01452965630190.03443188895020.07367924326450.03192214918930.0295594614029-0.00906015480925-0.22537891306-0.0907005610960.01373459189290.2700661465050.0440188238442-0.08523038584970.2136706801140.01516836907990.175060538176128.867456217227.16917678131.8643320516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 265)
2X-RAY DIFFRACTION2(chain 'B' and resid 24 through 265)
3X-RAY DIFFRACTION3(chain 'C' and resid 24 through 265)
4X-RAY DIFFRACTION4(chain 'D' and resid 24 through 265)

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